2GTA

Crystal Structure of the putative pyrophosphatase YPJD from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR428.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the putative pyrophosphatase YPJD from Bacillus subtilis.

Vorobiev, S.M.Zhou, W.Seetharaman, J.Wang, D.Ma, L.C.Acton, T.Xio, R.Montelione, G.T.Tong, L.Hunt, J.F.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein ypjD
A, B, C, D
119Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ypjD (jojD)
Find proteins for P42979 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42979
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.747α = 90.00
b = 79.694β = 90.00
c = 119.568γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
ADSCdata collection
SHELXDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-25
    Type: Author supporting evidence