Download MendeleyCharacterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from
Wei, Z., Wilkinson, R.C., Rashid, G.M.M., Brown, D., Fulop, V., Bugg, T.D.H.(2019) Biochemistry 58: 5281-5293
7ORX | pdb_00007orx
Rhodococcus jostii RHA1 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase
- PDB DOI: https://doi.org/10.2210/pdb7ORX/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Rhodococcus jostii RHA1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2021-06-06 Released: 2021-06-16
- Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.233 (Depositor), 0.230 (DCC)
- R-Value Work: 0.195 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.196 (Depositor)
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Probable benzoylformate decarboxylase | A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD] | 531 | Rhodococcus jostii RHA1 | Mutation(s): 0 Gene Names: RHA1_ro02985 EC: 4.1.1.7 (PDB Primary Data), 2.2.1.6 (UniProt) |  |
UniProt | |||||
Find proteins for Q0SCE8 (Rhodococcus jostii (strain RHA1)) Explore Q0SCE8 Go to UniProtKB: Q0SCE8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q0SCE8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TPP (Subject of Investigation/LOI) Query on TPP | E [auth AAA], G [auth BBB], I [auth CCC], K [auth DDD] | THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O |  | ||
| NA Query on NA | F [auth AAA], H [auth BBB], J [auth CCC], L [auth DDD] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| SEP Query on SEP | A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD] | L-PEPTIDE LINKING | C3 H8 N O6 P |  | SER |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.233 (Depositor), 0.230 (DCC)
- R-Value Work: 0.195 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.196 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 123.5 | α = 90 |
| b = 132.24 | β = 90 |
| c = 138.7 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-06-16 Deposition Author(s): Wilkinson, R.C., Fulop, V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Biotechnology and Biological Sciences Research Council (BBSRC) | United Kingdom | BB/M025772/1 |
| Biotechnology and Biological Sciences Research Council (BBSRC) | United Kingdom | BB/M003523/1 |
Revision History (Full details and data files)
- Version 1.0: 2021-06-16
Type: Initial release - Version 1.1: 2024-01-31
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2024-11-20
Changes: Structure summary
