3GZB

Crystal structure of putative SnoaL-like polyketide cyclase (YP_001182657.1) from Shewanella putrefaciens CN-32 at 1.44 A resolution

PDB DOI: https://doi.org/10.2210/pdb3GZB/pdb

Classification: LYASE
Organism(s): Shewanella putrefaciens CN-32
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-04-06 Released: 2009-04-21
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.174
R-Value Work: 0.151
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative SnoaL-like polyketide cyclase (YP_001182657.1) from Shewanella putrefaciens CN-32 at 1.44 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 146.99 kDa
Atom Count: 12,036
Modelled Residue Count: 1,164
Deposited Residue Count: 1,232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative SnoaL-like polyketide cyclase	A, B, C, D, E A, B, C, D, E, F, G, H	154	Shewanella putrefaciens CN-32	Mutation(s): 0 Gene Names: Sputcn32_1130, YP_001182657.1
UniProt
Find proteins for A4Y4H5 (Shewanella putrefaciens (strain CN-32 / ATCC BAA-453)) Explore A4Y4H5 Go to UniProtKB: A4Y4H5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4Y4H5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain ZA [auth H] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain ZA [auth H] mmCIF format, chain AA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain ZA [auth H]	AA [auth D] J [auth A] MA [auth F] NA [auth F] O [auth B] AA [auth D], J [auth A], MA [auth F], NA [auth F], O [auth B], ZA [auth H]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain O [auth B] Focus chain ZA [auth H]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain RA [auth G] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain GA [auth E] SDF format, chain I [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain RA [auth G] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain I [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain RA [auth G] mmCIF format, chain SA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain GA [auth E] mmCIF format, chain I [auth A]	FA [auth E] GA [auth E] HA [auth E] I [auth A] K [auth A] FA [auth E], GA [auth E], HA [auth E], I [auth A], K [auth A], RA [auth G], SA [auth G], TA [auth G], V [auth C], W [auth C], X [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain K [auth A] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain K [auth A] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BA [auth D] SDF format, chain BB [auth H] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain UA [auth G] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain YA [auth G] SDF format, chain Z [auth C] SDF format, chain T [auth B] SDF format, chain Y [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth H] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain AB [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth H] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth G] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C]	AB [auth H] BA [auth D] BB [auth H] CA [auth D] DA [auth D] AB [auth H], BA [auth D], BB [auth H], CA [auth D], DA [auth D], EA [auth D], IA [auth E], JA [auth E], KA [auth E], L [auth A], LA [auth E], M [auth A], N [auth A], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], S [auth B], T [auth B], U [auth B], UA [auth G], VA [auth G], WA [auth G], XA [auth G], Y [auth C], YA [auth G], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain BA [auth D] Focus chain BB [auth H] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth H] Focus chain BA [auth D] Focus chain BB [auth H] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain Z [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.174
R-Value Work: 0.151
R-Value Observed: 0.152
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33GZB

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.24	α = 90
b = 89.94	β = 89.94
c = 94.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-04-21
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: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Structure summary