4RB3 Metal Binding Protein Dna date Sep 12, 2014
title Crystal Structure Of Magnetospirillum Gryphiswaldense Msr-1 Feoab1 Operator
authors Z.Deng, Z.Chen
compound source
Molecule: Dna (25-Mer)
Chain: A
Synonym: Feoab1 Operator
Engineered: Yes
Synthetic: Yes

Molecule: Dna (25-Mer)
Chain: B
Synonym: Feoab1 Operator
Engineered: Yes

Synthetic: Yes

Molecule: Dna-Binding Transcriptional Dual Regulator Of Sid Biosynthesis And Transport(Fur Family);
Chain: C, D
Engineered: Yes
Mutation: Yes

Organism_scientific: Magnetospirillum Gryphiswaldense
Organism_taxid: 1430440
Strain: Msr-1 V2
Gene: Fur, Mgmsrv2_3137
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.232 R_Free 0.265
length a length b length c angle alpha angle beta angle gamma
93.995 68.642 83.995 90.00 108.70 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand MN, SO4 enzyme
D, C

Primary referenceMechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator., Deng Z, Wang Q, Liu Z, Zhang M, Machado AC, Chiu TP, Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi X, Li X, Wu W, Rohs R, Li Y, Chen Z, Nat Commun. 2015 Jul 2;6:7642. doi: 10.1038/ncomms8642. PMID:26134419
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (4rb3.pdb1.gz) 132 Kb
  • LPC: Ligand-Protein Contacts for 4RB3
  • CSU: Contacts of Structural Units for 4RB3
  • Structure Factors (120 Kb)
  • Retrieve 4RB3 in mmCIF format [Save to disk]
  • Re-refined 4rb3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RB3 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 4RB3
  • 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1h4rb3, region B:20-103 [Jmol] [rasmolscript] [script source]
  • Fold representative 4rb3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rb3_C] [4rb3_A] [4rb3_D] [4rb3_B] [4rb3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4RB3
  • Community annotation for 4RB3 at PDBWiki (http://pdbwiki.org)

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