Download MendeleyCrystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83.
Nocek, B., Mulligan, R., Moy, S., Joachimiak, A.To be published.
3BIO | pdb_00003bio
Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83
- PDB DOI: https://doi.org/10.2210/pdb3BIO/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Porphyromonas gingivalis W83
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2007-11-30 Released: 2007-12-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.187 (Depositor), 0.194 (DCC)
- R-Value Work: 0.156 (Depositor), 0.163 (DCC)
- R-Value Observed: 0.158 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Oxidoreductase, Gfo/Idh/MocA family | 304 | Porphyromonas gingivalis W83 | Mutation(s): 0 Gene Names: PG_0806 EC: 1.4.1.16 |  | |
UniProt | |||||
Find proteins for Q7MW40 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MW40 Go to UniProtKB: Q7MW40 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7MW40 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | D [auth A], F [auth B] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | C [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.187 (Depositor), 0.194 (DCC)
- R-Value Work: 0.156 (Depositor), 0.163 (DCC)
- R-Value Observed: 0.158 (Depositor)
Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 99.268 | α = 90 |
| b = 99.268 | β = 90 |
| c = 356.025 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELX | phasing |
| Coot | model building |
| MLPHARE | phasing |
| PHENIX | phasing |
| REFMAC | phasing |
| ARP/wARP | model building |
Entry History
Deposition Data
- Released Date: 2007-12-25 Deposition Author(s): Nocek, B., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-12-25
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary
