1YK4	Electron Transport	date	Jan 17, 2005
title	Ultra-High Resolution Structure Of Pyrococcus Abyssi Rubredo W4lr5s
authors	H.Bonisch, C.L.Schmidt, P.Bianco, R.Ladenstein
compound		source
Molecule: Rubredoxin Chain: A Synonym: Rd Engineered: Yes Mutation: Yes		Organism_scientific: Pyrococcus Abyssi Organism_taxid: 29292 Gene: Rub Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet15b
symmetry	Space Group: P 21 21 21	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 25.140 39.500 45.070 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	0.69 Å
ligand	FE	enzyme
note	1YK4 is a representative structure
Gene Ontology	Chain Function Process Component A electron transfer activity
Primary reference	Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S., Bonisch H, Schmidt CL, Bianco P, Ladenstein R, Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):990-1004. Epub 2005, Jun 24. PMID:15983423

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk] Biological Unit Coordinates (1yk4.pdb1.gz) 30 Kb LPC: Ligand-Protein Contacts for 1YK4 CSU: Contacts of Structural Units for 1YK4 Likely Quarternary Molecular Structure file(s) for 1YK4 Structure Factors (1359 Kb) Retrieve 1YK4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YK4 from S2C, [Save to disk] Re-refined 1yk4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YK4 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 1YK4

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1YK4, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1yk4_A] [1yk4] SWISS-PROT database: [Q9V099] Domain organization of [RUBR_PYRAB] by SWISSPFAM

Other resources with information on 1YK4

Community annotation for 1YK4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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