2OYO | pdb_00002oyo

Crystal structure of Uncharacterized peroxidase-related protein (YP_604910.1) from Deinococcus geothermalis DSM 11300 at 1.51 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OYO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Deinococcus geothermalis DSM 11300
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-02-22 Released: 2007-03-20 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of Uncharacterized peroxidase-related protein (YP_604910.1) from Deinococcus geothermalis DSM 11300 at 1.51 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 44.18 kDa 
• Atom Count: 3,389 
• Modeled Residue Count: 372 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized peroxidase-related protein	A, B	196	Deinococcus geothermalis DSM 11300	Mutation(s): 3  Gene Names: YP_604910.1, Dgeo_1446
UniProt
Find proteins for Q1IYE3 (Deinococcus geothermalis (strain DSM 11300 / CIP 105573 / AG-3a)) Explore Q1IYE3  Go to UniProtKB:  Q1IYE3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32OYO

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.649	α = 90
b = 135.649	β = 90
c = 118.084	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary