OCA Atlas for 3PCD

3PCD

Dioxygenase

date

Nov 24, 1997

title

Protocatechuate 3,4-Dioxygenase Y447h Mutant

authors

A.M.Orville, J.D.Lipscomb, D.H.Ohlendorf

compound

source

Molecule: Protocatechuate 3,4-Dioxygenase
Chain: A, B, C, D, E, F
Ec: 1.13.11.3
Engineered: Yes
Mutation: Yes

Organism_scientific: Pseudomonas Putida
Organism_taxid: 303
Atcc: 23975
Gene: Pcah
Expression_system: Pseudomonas Fluorescens
Expression_system_taxid: 294
Expression_system_plasmid: Prwf158-Tyr147his
Expression_system_gene: Pcah

Molecule: Protocatechuate 3,4-Dioxygenase
Chain: M, N, O, P, Q, R
Ec: 1.13.11.3
Engineered: Yes
Mutation: Yes

symmetry

Space Group: I 1 2 1

R_factor

0.180

R_Free

NULL

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
197.400	127.200	134.600	90.00	97.70	90.00

method

X-Ray Diffraction

resolution

2.10 Å

ligand

BME, CO3, FE

enzyme

Oxidoreductase E.C.1.13.11.3 BRENDA

related structures

by homologous chain: 3PCE, 3PCK

Gene
Ontology

Chain	Function	Process	Component
F, A, E, B, C, D
O, N, P, Q, M, R

Primary reference

The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates., Frazee RW, Orville AM, Dolbeare KB, Yu H, Ohlendorf DH, Lipscomb JD, Biochemistry 1998 Feb 24;37(8):2131-44. PMID:9485360

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (438 Kb) [Save to disk]

Biological Unit Coordinates (3pcd.pdb1.gz) 853 Kb

LPC: Ligand-Protein Contacts for 3PCD

CSU: Contacts of Structural Units for 3PCD

Likely Quarternary Molecular Structure file(s) for 3PCD

Retrieve 3PCD in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3PCD from S2C, [Save to disk]

View 3PCD 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 3PCD

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 3PCD, from MSDmotif at EBI

Genome occurence of 3PCD's fold from GeneCensus

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d3pcda_, region A [Jmol] [rasmolscript] [script source]
- Domain d3pcdb_, region B [Jmol] [rasmolscript] [script source]
- Domain d3pcdc_, region C [Jmol] [rasmolscript] [script source]
- Domain d3pcdd_, region D [Jmol] [rasmolscript] [script source]
- Domain d3pcde_, region E [Jmol] [rasmolscript] [script source]
- Domain d3pcdf_, region F [Jmol] [rasmolscript] [script source]
- Domain d3pcdm_, region M [Jmol] [rasmolscript] [script source]
- Domain d3pcdn_, region N [Jmol] [rasmolscript] [script source]
- Domain d3pcdo_, region O [Jmol] [rasmolscript] [script source]
- Domain d3pcdp_, region P [Jmol] [rasmolscript] [script source]
- Domain d3pcdq_, region Q [Jmol] [rasmolscript] [script source]
- Domain d3pcdr_, region R [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: [3pcd_E] [3pcd_N] [3pcd_Q] [3pcd_O] [3pcd_D] [3pcd_R] [3pcd_F] [3pcd_M] [3pcd_B] [3pcd_A] [3pcd_P] [3pcd_C] [3pcd]

SWISS-PROT database: [P00436] [P00437]

Domain organization of [PCXA_PSEPU] [PCXB_PSEPU] by SWISSPFAM

Other resources with information on 3PCD

Community annotation for 3PCD at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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