2HJG

The crystal structure of the B. subtilis YphC GTPase in complex with GDP

Structural Biology Knowledgebase: 2HJG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.215

Literature

Macromolecules
Sequence Display for 2HJG

Classification: HYDROLASE

Total Structure Weight: 50343.63

Macromolecule Entities
Molecule Chains Length Organism Details
GTP-binding protein engA A 436 Bacillus subtilis Mutation: M1M, M80M, M89M, M126M, M195M, M233M, M306M, M328M, M340M, M364M, M369M, M405M
Gene Name(s): der engA yphC BSU22840
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GDP
Query on GDP

A GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.215
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.71 α = 90.00
b = 65.04 β = 90.00
c = 110.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-30
  • Released Date: 2006-08-08
  • Deposition author(s): Muench, S.P., Xu, L., Sedelnikova, S.E., Rice, D.W

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4