2GTA

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

• PDB DOI: https://doi.org/10.2210/pdb2GTA/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-04-27 Released: 2006-05-23 
• Deposition Author(s): Vorobiev, S.M., Zhou, W., Seetharaman, J., Wang, D., Ma, L.C., Acton, T., Xio, R., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 

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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 57.47 kDa 
• Atom Count: 2,968 
• Modelled Residue Count: 377 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ypjD	A, B, C, D	119	Bacillus subtilis	Mutation(s): 6  Gene Names: ypjD
UniProt
Find proteins for P42979 (Bacillus subtilis (strain 168)) Explore P42979  Go to UniProtKB:  P42979

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A], F [auth B], G [auth C], H [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.747	α = 90
b = 79.694	β = 90
c = 119.568	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-23 
Deposition Author(s): Vorobiev, S.M., Zhou, W., Seetharaman, J., Wang, D., Ma, L.C., Acton, T., Xio, R., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

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