2DWC | pdb_00002dwc

Crystal structure of Probable phosphoribosylglycinamide formyl transferase from Pyrococcus horikoshii OT3 complexed with ADP

• PDB DOI: https://doi.org/10.2210/pdb2DWC/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-10 Released: 2007-02-10 
• Deposition Author(s): Yoshikawa, S., Arai, R., Kamo-Uchikubo, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Probable phosphoribosylglycinamide formyl transferase from Pyrococcus horikoshii OT3 complexed with ADP

Yoshikawa, S., Arai, R., Kamo-Uchikubo, T., Shirouzu, M., Yokoyama, S.

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 (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.79 kDa 
• Atom Count: 7,060 
• Modeled Residue Count: 815 
• Deposited Residue Count: 866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
433aa long hypothetical phosphoribosylglycinamide formyl transferase	A, B	433	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH0318 EC: 2.1.2 (PDB Primary Data), 6.3.1.21 (UniProt)
UniProt
Find proteins for O58056 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58056  Go to UniProtKB:  O58056

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	C [auth A], D [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.170 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.734	α = 90
b = 212.518	β = 90
c = 120.605	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-10 
Deposition Author(s): Yoshikawa, S., Arai, R., Kamo-Uchikubo, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-02-10
  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