3R89 | pdb_00003r89

Crystal structure of orotidine 5-phosphate decarboxylase from Anaerococcus prevotii DSM 20548

PDB DOI: https://doi.org/10.2210/pdb3R89/pdb

Classification: LYASE
Organism(s): Anaerococcus prevotii DSM 20548
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-03-23 Released: 2011-04-06
Deposition Author(s): Chang, C., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.197 (Depositor), 0.203 (DCC)
R-Value Work:
0.158 (Depositor), 0.166 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of orotidine 5'-phosphate decarboxylase from Anaerococcus prevotii DSM 20548

Chang, C., Tesar, C., Bearden, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 66.61 kDa
Atom Count: 5,241
Modeled Residue Count: 578
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	290	Anaerococcus prevotii DSM 20548	Mutation(s): 0 Gene Names: pyrF, Apre_0783 EC: 4.1.1.23
UniProt
Find proteins for C7RH50 (Anaerococcus prevotii (strain ATCC 9321 / DSM 20548 / JCM 6508 / NCTC 11806 / PC1)) Explore C7RH50 Go to UniProtKB: C7RH50
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7RH50
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.197 (Depositor), 0.203 (DCC)
R-Value Work: 0.158 (Depositor), 0.166 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.507	α = 90
b = 108.848	β = 90
c = 138.171	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.