2OGJ | pdb_00002ogj

Crystal structure of a dihydroorotase

PDB DOI: https://doi.org/10.2210/pdb2OGJ/pdb

Classification: HYDROLASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-01-05 Released: 2007-02-20
Deposition Author(s): Sugadev, R., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.302 (Depositor), 0.290 (DCC)
R-Value Work:
0.256 (Depositor), 0.240 (DCC)
R-Value Observed:
0.256 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a dihydroorotase

Sugadev, R., Kumaran, D., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 274.87 kDa
Atom Count: 16,585
Modeled Residue Count: 2,160
Deposited Residue Count: 2,502
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, E A, B, C, D, E, F	417	Agrobacterium fabrum str. C58	Mutation(s): 0 EC: 3.1.1
UniProt
Find proteins for Q7CS13 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CS13 Go to UniProtKB: Q7CS13
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7CS13
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	M [auth C], P [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain M [auth C] Focus chain P [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain Q [auth E] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], N [auth D], O [auth D], Q [auth E], R [auth E], S [auth F], T [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.302 (Depositor), 0.290 (DCC)
R-Value Work: 0.256 (Depositor), 0.240 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.65	α = 90
b = 139.2	β = 90
c = 206.13	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-02-20

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-02-20
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-12-27
Changes: Data collection, Database references