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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNL	B [auth A]	Unknown ligand

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.250 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32Q9K

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

Entry History 

Deposition Data

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

Revision History  

• 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