2DR3 | pdb_00002dr3

Crystal Structure of RecA superfamily ATPase PH0284 from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2DR3/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-06 Released: 2006-12-06 
• Deposition Author(s): Bagautdinov, B., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of RecA superfamily ATPase PH0284 from Pyrococcus horikoshii OT3

Bagautdinov, B., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 167.99 kDa 
• Atom Count: 12,543 
• Modeled Residue Count: 1,419 
• Deposited Residue Count: 1,482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0273 protein PH0284	A, B, C, D, E, F	247	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH0284
UniProt
Find proteins for O58022 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58022  Go to UniProtKB:  O58022

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.057	α = 90
b = 96.057	β = 90
c = 298.897	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-06 
Deposition Author(s): Bagautdinov, B., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description