2EF0 | pdb_00002ef0

Crystal structure of ornithine carbamoyltransferase from thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb2EF0/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-02-19 Released: 2007-04-13
Deposition Author(s): Karthe, P., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of ornithine carbamoyltransferase from thermus thermophilus

Karthe, P., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 33.33 kDa
Atom Count: 2,387
Modeled Residue Count: 287
Deposited Residue Count: 301
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A	301	Thermus thermophilus HB8	Mutation(s): 0 EC: 2.1.3.3
UniProt
Find proteins for Q5SJ15 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ15 Go to UniProtKB: Q5SJ15
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJ15
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.200 (Depositor), 0.199 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.385	α = 90
b = 77.385	β = 90
c = 79.132	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-04-13

Deposition Author(s):

Kumarevel, T.S.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-04-13
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.