3JZE

1.8 Angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

PDB DOI: https://doi.org/10.2210/pdb3JZE/pdb
Entry: 3JZE supersedes: 3IHN

Classification: HYDROLASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-09-23 Released: 2009-09-29
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.203 (Depositor), 0.220 (DCC)
R-Value Work:
0.163 (Depositor), 0.180 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (pyrC) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 168.02 kDa
Atom Count: 12,498
Modelled Residue Count: 1,372
Deposited Residue Count: 1,488
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotase	A, B, C, D	372	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: pyrC, STM1163 EC: 3.5.2.3
UniProt
Find proteins for P06204 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P06204 Go to UniProtKB: P06204
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06204
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain P [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain P [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain P [auth B]	DA [auth D], P [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain P [auth B] Interactions & Density Focus chain DA [auth D] Focus chain P [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain X [auth C] MOL2 format, chain J [auth A] MOL2 format, chain X [auth C] mmCIF format, chain J [auth A] mmCIF format, chain X [auth C]	J [auth A], X [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain X [auth C] Interactions & Density Focus chain J [auth A] Focus chain X [auth C]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	BA [auth D] CA [auth D] H [auth A] I [auth A] N [auth B] BA [auth D], CA [auth D], H [auth A], I [auth A], N [auth B], O [auth B], V [auth C], W [auth C]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	AA [auth D] E [auth A] F [auth A] L [auth B] M [auth B] AA [auth D], E [auth A], F [auth A], L [auth B], M [auth B], S [auth C], T [auth C], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C]	EA [auth D] FA [auth D] K [auth A] Q [auth B] R [auth B] EA [auth D], FA [auth D], K [auth A], Q [auth B], R [auth B], Y [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain U [auth C] MOL2 format, chain G [auth A] MOL2 format, chain U [auth C] mmCIF format, chain G [auth A] mmCIF format, chain U [auth C]	G [auth A], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain U [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.203 (Depositor), 0.220 (DCC)
R-Value Work: 0.163 (Depositor), 0.180 (DCC)
R-Value Observed: 0.165 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33jze

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.437	α = 90
b = 79.486	β = 90.35
c = 180.61	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-09-29

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

This entry supersedes: 3IHN

Revision History (Full details and data files)

Version 1.0: 2009-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, 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
Version 1.4: 2023-11-22
Changes: Data collection