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

Validation slider image for 3V75

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.