3KZW

Crystal structure of cytosol aminopeptidase from Staphylococcus aureus COL

PDB DOI: https://doi.org/10.2210/pdb3KZW/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-12-08 Released: 2010-01-12
Deposition Author(s): Hattne, J., Dubrovska, I., Halavaty, A., Minasov, G., Scott, P., Shuvalova, L., Winsor, J., Otwinowski, Z., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 686.36 kDa
Atom Count: 46,710
Modelled Residue Count: 5,927
Deposited Residue Count: 6,180
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosol aminopeptidase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	515	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: SACOL0945 EC: 3.4.11.1
UniProt
Find proteins for A0A0H2WYH0 (Staphylococcus aureus (strain COL)) Explore A0A0H2WYH0 Go to UniProtKB: A0A0H2WYH0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2WYH0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain IC [auth J] SDF format, chain MB [auth G] SDF format, chain QA [auth D] SDF format, chain T [auth A] MOL2 format, chain IC [auth J] MOL2 format, chain MB [auth G] MOL2 format, chain QA [auth D] MOL2 format, chain T [auth A] mmCIF format, chain IC [auth J] mmCIF format, chain MB [auth G] mmCIF format, chain QA [auth D] mmCIF format, chain T [auth A]	IC [auth J], MB [auth G], QA [auth D], T [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain IC [auth J] Focus chain MB [auth G] Focus chain QA [auth D] Focus chain T [auth A] Interactions & Density Focus chain IC [auth J] Focus chain MB [auth G] Focus chain QA [auth D] Focus chain T [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain AC [auth I] SDF format, chain BA [auth C] SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain CB [auth F] SDF format, chain CC [auth J] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain DC [auth J] SDF format, chain EA [auth C] SDF format, chain EC [auth J] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain FC [auth J] SDF format, chain GA [auth C] SDF format, chain GB [auth G] SDF format, chain GC [auth J] SDF format, chain HB [auth G] SDF format, chain IA [auth D] SDF format, chain IB [auth G] SDF format, chain JA [auth D] SDF format, chain JB [auth G] SDF format, chain JC [auth K] SDF format, chain KA [auth D] SDF format, chain KC [auth K] SDF format, chain LA [auth D] SDF format, chain LC [auth K] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MC [auth K] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain NB [auth H] SDF format, chain NC [auth K] SDF format, chain O [auth A] SDF format, chain OB [auth H] SDF format, chain OC [auth K] SDF format, chain P [auth A] SDF format, chain PB [auth H] SDF format, chain Q [auth A] SDF format, chain QB [auth H] SDF format, chain RA [auth E] SDF format, chain RB [auth H] SDF format, chain RC [auth L] SDF format, chain SA [auth E] SDF format, chain SB [auth H] SDF format, chain SC [auth L] SDF format, chain TA [auth E] SDF format, chain TC [auth L] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain UC [auth L] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain VB [auth I] SDF format, chain VC [auth L] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain WB [auth I] SDF format, chain X [auth B] SDF format, chain XB [auth I] SDF format, chain Y [auth B] SDF format, chain YB [auth I] SDF format, chain Z [auth B] SDF format, chain ZA [auth F] SDF format, chain ZB [auth I] MOL2 format, chain AB [auth F] MOL2 format, chain AC [auth I] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain CC [auth J] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain DC [auth J] MOL2 format, chain EA [auth C] MOL2 format, chain EC [auth J] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain FC [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain GC [auth J] MOL2 format, chain HB [auth G] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth G] MOL2 format, chain JC [auth K] MOL2 format, chain KA [auth D] MOL2 format, chain KC [auth K] MOL2 format, chain LA [auth D] MOL2 format, chain LC [auth K] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MC [auth K] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth H] MOL2 format, chain NC [auth K] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth H] MOL2 format, chain OC [auth K] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth H] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth H] MOL2 format, chain RC [auth L] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth H] MOL2 format, chain SC [auth L] MOL2 format, chain TA [auth E] MOL2 format, chain TC [auth L] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain UC [auth L] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain VB [auth I] MOL2 format, chain VC [auth L] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain WB [auth I] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth I] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth I] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth F] MOL2 format, chain ZB [auth I] mmCIF format, chain AB [auth F] mmCIF format, chain AC [auth I] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain CC [auth J] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain DC [auth J] mmCIF format, chain EA [auth C] mmCIF format, chain EC [auth J] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain FC [auth J] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth G] mmCIF format, chain GC [auth J] mmCIF format, chain HB [auth G] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth G] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth G] mmCIF format, chain JC [auth K] mmCIF format, chain KA [auth D] mmCIF format, chain KC [auth K] mmCIF format, chain LA [auth D] mmCIF format, chain LC [auth K] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain MC [auth K] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain NB [auth H] mmCIF format, chain NC [auth K] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth H] mmCIF format, chain OC [auth K] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth H] mmCIF format, chain RA [auth E] mmCIF format, chain RB [auth H] mmCIF format, chain RC [auth L] mmCIF format, chain SA [auth E] mmCIF format, chain SB [auth H] mmCIF format, chain SC [auth L] mmCIF format, chain TA [auth E] mmCIF format, chain TC [auth L] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain UC [auth L] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain VB [auth I] mmCIF format, chain VC [auth L] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain WB [auth I] mmCIF format, chain X [auth B] mmCIF format, chain XB [auth I] mmCIF format, chain Y [auth B] mmCIF format, chain YB [auth I] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth F] mmCIF format, chain ZB [auth I]	AB [auth F] AC [auth I] BA [auth C] BB [auth F] CA [auth C] AB [auth F], AC [auth I], BA [auth C], BB [auth F], CA [auth C], CB [auth F], CC [auth J], DA [auth C], DB [auth F], DC [auth J], EA [auth C], EC [auth J], FA [auth C], FB [auth G], FC [auth J], GA [auth C], GB [auth G], GC [auth J], HB [auth G], IA [auth D], IB [auth G], JA [auth D], JB [auth G], JC [auth K], KA [auth D], KC [auth K], LA [auth D], LC [auth K], M [auth A], MA [auth D], MC [auth K], N [auth A], NA [auth D], NB [auth H], NC [auth K], O [auth A], OB [auth H], OC [auth K], P [auth A], PB [auth H], Q [auth A], QB [auth H], RA [auth E], RB [auth H], RC [auth L], SA [auth E], SB [auth H], SC [auth L], TA [auth E], TC [auth L], U [auth B], UA [auth E], UC [auth L], V [auth B], VA [auth E], VB [auth I], VC [auth L], W [auth B], WA [auth E], WB [auth I], X [auth B], XB [auth I], Y [auth B], YB [auth I], Z [auth B], ZA [auth F], ZB [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth F] Focus chain AC [auth I] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain CC [auth J] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain DC [auth J] Focus chain EA [auth C] Focus chain EC [auth J] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain FC [auth J] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain GC [auth J] Focus chain HB [auth G] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain JC [auth K] Focus chain KA [auth D] Focus chain KC [auth K] Focus chain LA [auth D] Focus chain LC [auth K] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MC [auth K] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth H] Focus chain NC [auth K] Focus chain O [auth A] Focus chain OB [auth H] Focus chain OC [auth K] Focus chain P [auth A] Focus chain PB [auth H] Focus chain Q [auth A] Focus chain QB [auth H] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain RC [auth L] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain SC [auth L] Focus chain TA [auth E] Focus chain TC [auth L] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UC [auth L] Focus chain V [auth B] Focus chain VA [auth E] Focus chain VB [auth I] Focus chain VC [auth L] Focus chain W [auth B] Focus chain WA [auth E] Focus chain WB [auth I] Focus chain X [auth B] Focus chain XB [auth I] Focus chain Y [auth B] Focus chain YB [auth I] Focus chain Z [auth B] Focus chain ZA [auth F] Focus chain ZB [auth I] Interactions & Density Focus chain AB [auth F] Focus chain AC [auth I] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain CC [auth J] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain DC [auth J] Focus chain EA [auth C] Focus chain EC [auth J] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain FC [auth J] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain GC [auth J] Focus chain HB [auth G] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain JC [auth K] Focus chain KA [auth D] Focus chain KC [auth K] Focus chain LA [auth D] Focus chain LC [auth K] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MC [auth K] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth H] Focus chain NC [auth K] Focus chain O [auth A] Focus chain OB [auth H] Focus chain OC [auth K] Focus chain P [auth A] Focus chain PB [auth H] Focus chain Q [auth A] Focus chain QB [auth H] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain RC [auth L] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain SC [auth L] Focus chain TA [auth E] Focus chain TC [auth L] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UC [auth L] Focus chain V [auth B] Focus chain VA [auth E] Focus chain VB [auth I] Focus chain VC [auth L] Focus chain W [auth B] Focus chain WA [auth E] Focus chain WB [auth I] Focus chain X [auth B] Focus chain XB [auth I] Focus chain Y [auth B] Focus chain YB [auth I] Focus chain Z [auth B] Focus chain ZA [auth F] Focus chain ZB [auth I]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BC [auth I] SDF format, chain EB [auth F] SDF format, chain HA [auth C] SDF format, chain HC [auth J] SDF format, chain KB [auth G] SDF format, chain LB [auth G] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain PC [auth K] SDF format, chain QC [auth K] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain TB [auth H] SDF format, chain UB [auth H] SDF format, chain WC [auth L] SDF format, chain XA [auth E] SDF format, chain XC [auth L] SDF format, chain YA [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain BC [auth I] MOL2 format, chain EB [auth F] MOL2 format, chain HA [auth C] MOL2 format, chain HC [auth J] MOL2 format, chain KB [auth G] MOL2 format, chain LB [auth G] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain PC [auth K] MOL2 format, chain QC [auth K] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain TB [auth H] MOL2 format, chain UB [auth H] MOL2 format, chain WC [auth L] MOL2 format, chain XA [auth E] MOL2 format, chain XC [auth L] MOL2 format, chain YA [auth E] mmCIF format, chain AA [auth B] mmCIF format, chain BC [auth I] mmCIF format, chain EB [auth F] mmCIF format, chain HA [auth C] mmCIF format, chain HC [auth J] mmCIF format, chain KB [auth G] mmCIF format, chain LB [auth G] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain PC [auth K] mmCIF format, chain QC [auth K] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain TB [auth H] mmCIF format, chain UB [auth H] mmCIF format, chain WC [auth L] mmCIF format, chain XA [auth E] mmCIF format, chain XC [auth L] mmCIF format, chain YA [auth E]	AA [auth B] BC [auth I] EB [auth F] HA [auth C] HC [auth J] AA [auth B], BC [auth I], EB [auth F], HA [auth C], HC [auth J], KB [auth G], LB [auth G], OA [auth D], PA [auth D], PC [auth K], QC [auth K], R [auth A], S [auth A], TB [auth H], UB [auth H], WC [auth L], XA [auth E], XC [auth L], YA [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BC [auth I] Focus chain EB [auth F] Focus chain HA [auth C] Focus chain HC [auth J] Focus chain KB [auth G] Focus chain LB [auth G] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain PC [auth K] Focus chain QC [auth K] Focus chain R [auth A] Focus chain S [auth A] Focus chain TB [auth H] Focus chain UB [auth H] Focus chain WC [auth L] Focus chain XA [auth E] Focus chain XC [auth L] Focus chain YA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain BC [auth I] Focus chain EB [auth F] Focus chain HA [auth C] Focus chain HC [auth J] Focus chain KB [auth G] Focus chain LB [auth G] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain PC [auth K] Focus chain QC [auth K] Focus chain R [auth A] Focus chain S [auth A] Focus chain TB [auth H] Focus chain UB [auth H] Focus chain WC [auth L] Focus chain XA [auth E] Focus chain XC [auth L] Focus chain YA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.222 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33kzw

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.383	α = 90
b = 154.733	β = 90
c = 340.101	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-01-12

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description