2Q9K | pdb_00002q9k

Crystal structure of a putative oxidoreductase (exig_1997) from exiguobacterium sibiricum 255-15 at 1.59 A resolution

PDB DOI: https://doi.org/10.2210/pdb2Q9K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Exiguobacterium artemiae 255-15
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-06-12 Released: 2007-06-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.252 (Depositor), 0.253 (DCC)
R-Value Work:
0.203 (Depositor), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2Q9K

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of conserved uncharacterized protein (ZP_00539648.1) from Exiguobacterium sp. 255-15 at 1.59 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 17.28 kDa
Atom Count: 1,348
Modeled Residue Count: 147
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	151	Exiguobacterium artemiae 255-15	Mutation(s): 3 Gene Names: ZP_00539648.1, ExigDRAFT_1246
UniProt
Find proteins for B1YJ68 (Exiguobacterium sibiricum (strain DSM 17290 / CCUG 55495 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YJ68 Go to UniProtKB: B1YJ68
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1YJ68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNL Query on UNL Download:Ideal Coordinates CCD File	B [auth A]	Unknown ligand		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.59 Å
R-Value Free: 0.252 (Depositor), 0.253 (DCC)
R-Value Work: 0.203 (Depositor), 0.205 (DCC)
R-Value Observed: 0.206 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.314	α = 90
b = 56.314	β = 90
c = 95.205	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-06-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
Version 1.6: 2024-10-30
Changes: Data collection, Structure summary

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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.