5B3F Transferase date Feb 22, 2016
title Crystal Structure Of Phosphoribulokinase From Methanospirill Hungatei
authors H.Matsumura, H.Ashida
compound source
Molecule: Phosphoribulokinaseuridine Kinase
Chain: A, B
Engineered: Yes
Organism_scientific: Methanospirillum Hungatei Jf-1
Organism_taxid: 323259
Strain: Jf-1
Gene: Mhun_0794
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.279
length a length b length c angle alpha angle beta angle gamma
78.414 93.822 99.942 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand SO4 enzyme
A, B

Primary referenceA RuBisCO-mediated carbon metabolic pathway in methanogenic archaea., Kono T, Mehrotra S, Endo C, Kizu N, Matusda M, Kimura H, Mizohata E, Inoue T, Hasunuma T, Yokota A, Matsumura H, Ashida H, Nat Commun. 2017 Jan 13;8:14007. doi: 10.1038/ncomms14007. PMID:28082747
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (5b3f.pdb1.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 5B3F
  • CSU: Contacts of Structural Units for 5B3F
  • Structure Factors (321 Kb)
  • Retrieve 5B3F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B3F from S2C, [Save to disk]
  • Re-refined 5b3f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5B3F 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 5B3F
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5b3f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5b3f] [5b3f_A] [5b3f_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5B3F
  • Community annotation for 5B3F at PDBWiki (http://pdbwiki.org)

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