2E18 | pdb_00002e18

Crystal structure of project PH0182 from Pyrococcus horikoshii OT3

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2E18

This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of project PH0182 from Pyrococcus horikoshii OT3

Shimizu, K., Kunishima, N.

To be published.

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NH(3)-dependent NAD(+) synthetase
A, B
257Pyrococcus horikoshii OT3Mutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO57921
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD

Query on IMD


Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]		IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN

Query on ZN


Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
J [auth B]
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), 0.262 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.919α = 90
b = 84.919β = 90
c = 113.576γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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