3V75 | pdb_00003v75

Crystal structure of putative orotidine 5'-phosphate decarboxylase from Streptomyces avermitilis ma-4680

PDB DOI: https://doi.org/10.2210/pdb3V75/pdb
Entry: 3V75 supersedes: 3L52

Classification: LYASE
Organism(s): Streptomyces avermitilis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-12-20 Released: 2012-05-09
Deposition Author(s): Stogios, P.J., Xu, X., Cui, H., Kudritska, M., Tan, K., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.172 (Depositor), 0.167 (DCC)
R-Value Work:
0.148 (Depositor), 0.142 (DCC)
R-Value Observed:
0.149 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of putative orotidine 5'-phosphate decarboxylase from Streptomyces avermitilis ma-4680

Stogios, P.J., Xu, X., Cui, H., Kudritska, M., Tan, K., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 31.68 kDa
Atom Count: 2,531
Modeled Residue Count: 285
Deposited Residue Count: 301
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	301	Streptomyces avermitilis	Mutation(s): 0 Gene Names: pyrF, SAV6869, SAV_6869 EC: 4.1.1.23
UniProt
Find proteins for Q827Q5 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q827Q5 Go to UniProtKB: Q827Q5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q827Q5
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.172 (Depositor), 0.167 (DCC)
R-Value Work: 0.148 (Depositor), 0.142 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.882	α = 90
b = 83.342	β = 110.52
c = 44.081	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-05-09

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 3L52

Revision History (Full details and data files)

Version 1.0: 2012-05-09
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-11-20
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.