1YKM	Oxidoreductase	date	Jan 18, 2005
title	Protocatechuate 3,4-Dioxygenase Y408e 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 0.169 R_Free 0.199
crystal cell	length a length b length c angle alpha angle beta angle gamma 196.612 127.728 134.321 90.00 97.66 90.00
method	X-Ray Diffraction	resolution	2.22 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] (447 Kb) [Save to disk] Biological Unit Coordinates (1ykm.pdb1.gz) 859 Kb LPC: Ligand-Protein Contacts for 1YKM CSU: Contacts of Structural Units for 1YKM Likely Quarternary Molecular Structure file(s) for 1YKM Structure Factors (921 Kb) Retrieve 1YKM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YKM from S2C, [Save to disk] Re-refined 1ykm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YKM 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 1YKM

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 1YKM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ykm_C] [1ykm_B] [1ykm_F] [1ykm_E] [1ykm_J] [1ykm_L] [1ykm_H] [1ykm_G] [1ykm_K] [1ykm_I] [1ykm] [1ykm_A] [1ykm_D] SWISS-PROT database: [P00436] [P00437] Domain organization of [PCXA_PSEPU] [PCXB_PSEPU] by SWISSPFAM

Other resources with information on 1YKM

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

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