3GD5 | pdb_00003gd5

Crystal structure of ornithine carbamoyltransferase from Gloeobacter violaceus

PDB DOI: https://doi.org/10.2210/pdb3GD5/pdb

Classification: TRANSFERASE
Organism(s): Gloeobacter violaceus PCC 7421
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-23 Released: 2009-04-14
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Ramagopal, U.A., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.239 (Depositor), 0.239 (DCC)
R-Value Observed:
0.240 (Depositor)

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

Literature

Crystal structure of ornithine carbamoyltransferase from Gloeobacter violaceus

Fedorov, A.A., Fedorov, E.V., Toro, R., Ramagopal, U.A., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 211.28 kDa
Atom Count: 13,303
Modeled Residue Count: 1,710
Deposited Residue Count: 1,938
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A, B, C, D, E A, B, C, D, E, F	323	Gloeobacter violaceus PCC 7421	Mutation(s): 0 Gene Names: argF, gll3101 EC: 2.1.3.3
UniProt
Find proteins for Q7NGR7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NGR7 Go to UniProtKB: Q7NGR7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NGR7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.271 (Depositor), 0.271 (DCC)
R-Value Work: 0.239 (Depositor), 0.239 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.563	α = 90
b = 142.423	β = 90
c = 149.273	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
Auto-Rickshaw	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-04-14

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references

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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.