1YKK	Oxidoreductase	date	Jan 18, 2005
title	Protocatechuate 3,4-Dioxygenase Y408c Mutant
authors	C.K.Brown, D.H.Ohlendorf
compound		source
Molecule: Protocatechuate 3,4-Dioxygenase Alpha Chain Chain: A, C, E, G, I, K Synonym: 3,4-Pcd Ec: 1.13.11.3 Engineered: Yes		Organism_scientific: Pseudomonas Putida Organism_taxid: 303 Gene: Pcag Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Protocatechuate 3,4-Dioxygenase Beta Chain Chain: B, D, F, H, J, L Synonym: 3,4-Pcd Ec: 1.13.11.3 Engineered: Yes Mutation: Yes		Organism_scientific: Pseudomonas Putida Organism_taxid: 303 Gene: Pcah Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: I 1 2 1	R_factor 0.210 R_Free 0.219
crystal cell	length a length b length c angle alpha angle beta angle gamma 194.870 126.961 132.764 90.00 96.39 90.00
method	X-Ray Diffraction	resolution	2.06 Å
ligand	CME, FE	enzyme	Oxidoreductase E.C.1.13.11.3 BRENDA
Gene Ontology	Chain Function Process Component A, K, E, C, I, G F, J, B, H, D, L
Primary reference	Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis., Valley MP, Brown CK, Burk DL, Vetting MW, Ohlendorf DH, Lipscomb JD, Biochemistry 2005 Aug 23;44(33):11024-39. PMID:16101286

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (429 Kb) [Save to disk] Biological Unit Coordinates (1ykk.pdb1.gz) 839 Kb LPC: Ligand-Protein Contacts for 1YKK CSU: Contacts of Structural Units for 1YKK Likely Quarternary Molecular Structure file(s) for 1YKK Structure Factors (1693 Kb) Retrieve 1YKK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YKK from S2C, [Save to disk] Re-refined 1ykk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YKK 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 1YKK

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 1YKK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ykk_I] [1ykk_J] [1ykk] [1ykk_A] [1ykk_C] [1ykk_B] [1ykk_D] [1ykk_L] [1ykk_F] [1ykk_E] [1ykk_H] [1ykk_K] [1ykk_G] SWISS-PROT database: [P00436] [P00437] Domain organization of [PCXA_PSEPU] [PCXB_PSEPU] by SWISSPFAM

Other resources with information on 1YKK

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

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