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- Structure Factors (CIF)
- Structure Factors (CIF - gz)
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- Validation (CIF - gz)
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- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
3T67|pdb_00003t67
Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
- PDB DOI: https://doi.org/10.2210/pdb3T67/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Pseudomonas putida
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-07-28 Released: 2012-08-01
- Deposition Author(s): Purpero, V.M.,Lipscomb, J.D.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.67 Å
- R-Value Free: 0.189 (Depositor), 0.190 (DCC)
- R-Value Work: 0.165 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.166 (Depositor)
Starting Model:experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
Download MendeleyAxial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Purpero, V.M., Lipscomb, J.D.To be published.
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 PISA (software)
Macromolecule Content
- Total Structure Weight: 148.01 kDa
- Atom Count: 11,464
- Modelled Residue Count: 1,314
- Deposited Residue Count: 1,314
- Unique protein chains: 2
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Protocatechuate 3,4-dioxygenase alpha chain | 200 | Pseudomonas putida | Mutation(s): 0 Gene Names: pcaG EC: 1.13.11.3 |  | |
UniProt | |||||
Find proteins for P00436 (Pseudomonas putida) Explore P00436 Go to UniProtKB: P00436 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00436 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Protocatechuate 3,4-dioxygenase beta chain | D [auth M], E [auth N], F [auth O] | 238 | Pseudomonas putida | Mutation(s): 0 Gene Names: pcaH EC: 1.13.11.3 |  |
UniProt | |||||
Find proteins for P00437 (Pseudomonas putida) Explore P00437 Go to UniProtKB: P00437 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00437 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CAQ Query on CAQ Download Ideal Coordinates CCD File
| L [auth C], N [auth M], P [auth N], R [auth O] | CATECHOL C6 H6 O2 YCIMNLLNPGFGHC-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 Download Ideal Coordinates CCD File | G [auth A], I [auth B], J [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL Download Ideal Coordinates CCD File | H [auth A], K [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| FE Query on FE Download Ideal Coordinates CCD File | M, O [auth N], Q [auth O] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.67 Å
- R-Value Free: 0.189 (Depositor), 0.190 (DCC)
- R-Value Work: 0.165 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.166 (Depositor)
Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 128.009 | α = 90 |
| b = 140.782 | β = 90 |
| c = 168.189 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data collection |
| HKL-3000 | data reduction |
Entry History
Deposition Data
- Released Date: 2012-08-01 Deposition Author(s): Purpero, V.M.,Lipscomb, J.D.
Revision History (Full details and data files)
- Version 1.0: 2012-08-01
Type: Initial release - Version 1.1: 2017-11-08
Changes: Refinement description - Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
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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.