- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- PDB Format
- PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full PDF
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
2BUQ|pdb_00002buq
Crystal Structure Of Wild-Type Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 in Complex with Catechol
- PDB DOI: https://doi.org/10.2210/pdb2BUQ/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Acinetobacter baylyi ADP1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2005-06-17 Released: 2006-09-05
- Deposition Author(s): Vetting, M.W.,Valley, M.P.,D'Argenio, D.A.,Ornston, L.N.,Lipscomb, J.D.,Ohlendorf, D.H.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.194 (Depositor), 0.180 (DCC)
- R-Value Work: 0.165 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.165 (Depositor)
Starting Model:experimental
View more details
wwPDB Validation 3D Report Full Report
Download MendeleyBiophysical Analyses of Designed and Selected Mutants of Protocatechuate 3,4-Dioxygenase
Brown, C.K., Vetting, M.W., Earhart, C.A., Ohlendorf, D.H.(2004) Annu Rev Microbiol 58: 555-585
- PubMed: 15487948 Search on PubMed
- DOI: https://doi.org/10.1146/annurev.micro.57.030502.090927
- Primary Citation of Related Structures:
2BUM,2BUQ,2BUR,2BUT,2BUV - PubMed Abstract:
The catechol dioxygenases allow a wide variety of bacteria to use aromatic compounds as carbon sources by catalyzing the key ring-opening step. These enzymes use specifically either catechol or protocatechuate (2,3-dihydroxybenozate) as their substrates; they use a bare metal ion as the sole cofactor. To learn how this family of metalloenzymes functions, a structural analysis of designed and selected mutants of these enzymes has been undertaken. Here we review the results of this analysis on the nonheme ferric iron intradiol dioxygenase protocatechuate 3,4-dioxygenase.
Organizational Affiliation:
Center for Metals in Biocatalysis and Department of Biochemistry, Molecular Biology, and Biophysics , Minneapolis, Minnesota 55455, USA. brow0927@umn.edu
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (CAQ)
Global Symmetry: Tetrahedral - T (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12
Pseudo Symmetry: Tetrahedral - T (Explore in 3D)
Pseudo Stoichiometry: Homo 24-mer - A24
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PQS (software)
Macromolecule Content
- Total Structure Weight: 51.37 kDa
- Atom Count: 3,797
- Modelled Residue Count: 440
- Deposited Residue Count: 450
- Unique protein chains: 2
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN | 209 | Acinetobacter baylyi ADP1 | Mutation(s): 0 EC: 1.13.11.3 |  | |
UniProt | |||||
Find proteins for P20371 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P20371 Go to UniProtKB: P20371 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P20371 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN | 241 | Acinetobacter baylyi ADP1 | Mutation(s): 0 EC: 1.13.11.3 |  | |
UniProt | |||||
Find proteins for P20372 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P20372 Go to UniProtKB: P20372 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P20372 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CAQ Query on CAQ Download Ideal Coordinates CCD File | D [auth B], E [auth B] | CATECHOL C6 H6 O2 YCIMNLLNPGFGHC-UHFFFAOYSA-N |  | ||
| FE Query on FE Download Ideal Coordinates CCD File | C [auth B] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.194 (Depositor), 0.180 (DCC)
- R-Value Work: 0.165 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.165 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 144.7 | α = 90 |
| b = 144.7 | β = 90 |
| c = 144.7 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
| CNS | phasing |
Deposition Data
- Released Date: 2006-09-05 Deposition Author(s): Vetting, M.W.,Valley, M.P.,D'Argenio, D.A.,Ornston, L.N.,Lipscomb, J.D.,Ohlendorf, D.H.
Revision History (Full details and data files)
- Version 1.0: 2006-09-05
Type: Initial release - Version 1.1: 2011-05-08
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2018-06-20
Changes: Data collection, Database references - Version 1.4: 2019-05-22
Changes: Data collection, Refinement description - Version 1.5: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
RCSB PDB is hosted by
RCSB PDB is a member of the
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.