1QYB	Electron Transport	date	Sep 10, 2003
title	X-Ray Crystal Structure Of Desulfovibrio Vulgaris Rubrerythr Zinc Substituted Into The [Fe(Scys)4] Site And Alternative Site Structures
authors	S.Jin, D.M.Kurtz, Z.J.Liu, J.Rose, B.C.Wang
compound		source
Molecule: Rubrerythrin Chain: A Engineered: Yes		Organism_scientific: Desulfovibrio Vulgaris Subsp. Vulgaris Organism_taxid: 882 Strain: Hildenborough Gene: Rr Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7-7
symmetry	Space Group: I 2 2 2	R_factor 0.182 R_Free 0.213
crystal cell	length a length b length c angle alpha angle beta angle gamma 48.008 80.161 101.029 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.75 Å
ligand	FE, SO4, ZN	enzyme
related structures	by homologous chain: 1B71, 1S2Z
Gene Ontology	Chain Function Process Component A
Primary reference	X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures., Jin S, Kurtz DM Jr, Liu ZJ, Rose J, Wang BC, Biochemistry 2004 Mar 23;43(11):3204-13. PMID:15023070

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk] Biological Unit Coordinates (1qyb.pdb1.gz) 70 Kb Biological Unit Coordinates (1qyb.pdb2.gz) 139 Kb LPC: Ligand-Protein Contacts for 1QYB CSU: Contacts of Structural Units for 1QYB Likely Quarternary Molecular Structure file(s) for 1QYB Structure Factors (314 Kb) Retrieve 1QYB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1QYB from S2C, [Save to disk] Re-refined 1qyb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1QYB 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 1QYB

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 1QYB, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1qyba2, region A:148-191 [Jmol] [rasmolscript] [script source]     - Domain d1qyba1, region A:2-147 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1qyb] [1qyb_A] SWISS-PROT database: [P24931] Domain organization of [RUBY_DESVH] by SWISSPFAM

Other resources with information on 1QYB

Community annotation for 1QYB at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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