3KD9 | pdb_00003kd9

Crystal structure of pyridine nucleotide disulfide oxidoreductase from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb3KD9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-22 Released: 2009-11-10
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.284 (Depositor), 0.281 (DCC)
R-Value Work:
0.244 (Depositor), 0.243 (DCC)
R-Value Observed:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3KD9

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

Literature

Crystal structure of pyridine nucleotide disulfide oxidoreductase from Pyrococcus horikoshii

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 148.73 kDa
Atom Count: 9,568
Modeled Residue Count: 1,254
Deposited Residue Count: 1,347
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme A disulfide reductase	A, B, C	449	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH0572 EC: 1.8.1.14 (PDB Primary Data), 1.8.1 (UniProt)
UniProt
Find proteins for O58308 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58308 Go to UniProtKB: O58308
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58308
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.284 (Depositor), 0.281 (DCC)
R-Value Work: 0.244 (Depositor), 0.243 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.81	α = 90
b = 114.81	β = 90
c = 353.917	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
Coot	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 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.