2E18 | pdb_00002e18

Crystal structure of project PH0182 from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2E18/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii OT3
• Mutation(s): No 


• Deposited: 2006-10-18 Released: 2007-04-24 
• Deposition Author(s): Shimizu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of project PH0182 from Pyrococcus horikoshii OT3

Shimizu, K., Kunishima, N.

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)

Macromolecule Content 

• Total Structure Weight: 58.4 kDa 
• Atom Count: 4,508 
• Modeled Residue Count: 512 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A, B	257	Pyrococcus horikoshii OT3	Mutation(s): 0  EC: 6.3.1.5
UniProt
Find proteins for O57921 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57921  Go to UniProtKB:  O57921

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	G [auth A], H [auth A], I [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.919	α = 90
b = 84.919	β = 90
c = 113.576	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Shimizu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-04-24
  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