3G5J Nucleotide Binding Protein date Feb 05, 2009
title Crystal Structure Of N-Terminal Domain Of Putative Atpgtp B Protein From Clostridium Difficile 630
authors B.Nocek, L.Bigelow, G.Cobb, A.Joachimiak, Midwest Center For Str Genomics (Mcsg)
compound source
Molecule: Putative Atpgtp Binding Protein
Chain: A, B
Fragment: Unp Residues 1-131
Engineered: Yes
 Organism_scientific: Clostridium Difficile
Organism_taxid: 272563
Strain: 630
Gene: Cd1325
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg19
symmetry Space Group: C 1 2 1
R_factor 0.172 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.489 60.192 79.107 90.00 108.62 90.00
method X-Ray Diffractionresolution 1.76 Å
ligand GOL, MSE, PGE enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (3g5j.pdb1.gz) 25 Kb
  • Biological Unit Coordinates (3g5j.pdb2.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 3G5J
  • CSU: Contacts of Structural Units for 3G5J
  • Likely Quarternary Molecular Structure file(s) for 3G5J
  • Structure Factors (812 Kb)
  • Retrieve 3G5J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G5J from S2C, [Save to disk]
  • Re-refined 3g5j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3G5J in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3G5J
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3G5J, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g5j_A] [3g5j] [3g5j_B]
  • SWISS-PROT database: [Q18BI8]
  • Domain organization of [Q18BI8_CLOD6] by SWISSPFAM
  • Domain found in 3G5J: [RHOD ] by SMART
    • Other resources with information on 3G5J
  • Community annotation for 3G5J at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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