2DCL | pdb_00002dcl

Structure of PH1503 protein from Pyrococcus Horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2DCL/pdb

• Classification: Structural genomics, unknown function
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-08 Released: 2006-07-08 
• 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: 2.28 Å
• R-Value Free: 
  0.290 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PH1503 protein from Pyrococcus Horikoshii OT3

Bagautdinov, B., Kunishima, N.

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: 45 kDa 
• Atom Count: 2,562 
• Modeled Residue Count: 294 
• Deposited Residue Count: 381 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical UPF0166 protein PH1503	A, B, C	127	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH1503
UniProt
Find proteins for O59172 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59172  Go to UniProtKB:  O59172

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	D [auth A], E [auth B], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.290 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.562	α = 90
b = 59.647	β = 122.47
c = 66.738	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-08 
Deposition Author(s): Bagautdinov, B., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2019-12-25
  Changes: Data collection
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description