2CU0 | pdb_00002cu0

Crystal structure of inosine-5'-monophosphate dehydrogenase from Pyrococcus horikoshii OT3

PDB DOI: https://doi.org/10.2210/pdb2CU0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-05-24 Released: 2006-05-24
Deposition Author(s): Asada, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.228 (Depositor), 0.229 (DCC)
R-Value Work:
0.205 (Depositor), 0.206 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of inosine-5'-monophosphate dehydrogenase from Pyrococcus horikoshii OT3

Asada, Y., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 106.74 kDa
Atom Count: 5,834
Modeled Residue Count: 713
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B	486	Pyrococcus horikoshii	Mutation(s): 0 EC: 1.1.1.205
UniProt
Find proteins for O58045 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58045 Go to UniProtKB: O58045
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58045
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XMP Query on XMP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	XANTHOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₄ O₉ P DCTLYFZHFGENCW-UUOKFMHZSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.228 (Depositor), 0.229 (DCC)
R-Value Work: 0.205 (Depositor), 0.206 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.666	α = 90
b = 123.666	β = 90
c = 130.053	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-05-24

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-05-24
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, 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.