3FDZ Isomerase date Nov 26, 2008
title Crystal Structure Of Phosphoglyceromutase From Burkholderia Pseudomallei 1710b With Bound 2,3-Diphosphoglyceric Acid An Phosphoglyceric Acid
authors Seattle Structural Genomics Center For Infectious Disease (S
compound source
Molecule: 2,3-Bisphosphoglycerate-Dependent Phosphoglycerat
Chain: A
Synonym: Phosphoglyceromutase, Pgam, Bpg-Dependent Pgam, Dp
Ec: 5.4.2.1
Engineered: Yes
Organism_scientific: Burkholderia Pseudomallei 1710b
Organism_taxid: 320372
Strain: 1719b
Gene: Burps1710b_0662, Gpma
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ava0421

Molecule: 2,3-Bisphosphoglycerate-Dependent Phosphoglycerat
Chain: B
Synonym: Phosphoglyceromutase, Pgam, Bpg-Dependent Pgam, Dp
Ec: 5.4.2.1
Engineered: Yes

Organism_scientific: Burkholderia Pseudomallei 1710b
Organism_taxid: 320372
Strain: 1719b
Gene: Burps1710b_0662, Gpma
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ava0421
symmetry Space Group: P 1
R_factor 0.183 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.390 48.480 62.090 106.03 91.54 107.50
method X-Ray Diffractionresolution 2.25 Å
ligand 3PG, DG2, NEP, PEG enzyme Isomerase E.C.5.4.2.1 BRENDA
Gene BURPS1710B
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAn ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase., Davies DR, Staker BL, Abendroth JA, Edwards TE, Hartley R, Leonard J, Kim H, Rychel AL, Hewitt SN, Myler PJ, Stewart LJ, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Sep 1;67(Pt, 9):1044-50. Epub 2011 Aug 13. PMID:21904048
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (3fdz.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (3fdz.pdb2.gz) 40 Kb
  • Biological Unit Coordinates (3fdz.pdb3.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 3FDZ
  • CSU: Contacts of Structural Units for 3FDZ
  • Likely Quarternary Molecular Structure file(s) for 3FDZ
  • Structure Factors (296 Kb)
  • Retrieve 3FDZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FDZ from S2C, [Save to disk]
  • Re-refined 3fdz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FDZ 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 3FDZ
  • 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 3FDZ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fdz_B] [3fdz_A] [3fdz]
  • SWISS-PROT database: [Q3JWH7]
  • Domain organization of [GPMA_BURP1] by SWISSPFAM
  • Domain found in 3FDZ: [PGAM ] by SMART
  • Other resources with information on 3FDZ
  • Community annotation for 3FDZ 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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