Download MendeleyThe structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides thetaiotaomicron VPI-5482
Cuff, M.E., Duggan, E., Abdullah, J., Joachimiak, A.To be published.
3DDH | pdb_00003ddh
The structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides thetaiotaomicron VPI-5482
- PDB DOI: https://doi.org/10.2210/pdb3DDH/pdb
- Classification: HYDROLASE
- Organism(s): Bacteroides thetaiotaomicron
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-06-05 Released: 2008-09-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.223 (Depositor), 0.230 (DCC)
- R-Value Work: 0.177 (Depositor), 0.183 (DCC)
- R-Value Observed: 0.179 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.4 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 |
| Putative haloacid dehalogenase-like family hydrolase | 234 | Bacteroides thetaiotaomicron | Mutation(s): 0 Gene Names: BT_2180 |  | |
UniProt | |||||
Find proteins for Q8A5Q8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A5Q8 Go to UniProtKB: Q8A5Q8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8A5Q8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | F [auth A], J [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A], I [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | C [auth A], E [auth A], G [auth B], H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| 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: 2.00 Å
- R-Value Free: 0.223 (Depositor), 0.230 (DCC)
- R-Value Work: 0.177 (Depositor), 0.183 (DCC)
- R-Value Observed: 0.179 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 36.119 | α = 90 |
| b = 104.222 | β = 90 |
| c = 121.212 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MLPHARE | phasing |
| DM | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELXD | phasing |
| SHELXE | model building |
| SOLVE | phasing |
| RESOLVE | phasing |
| ARP/wARP | model building |
| CCP4 | phasing |
| O | model building |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2008-09-30 Deposition Author(s): Cuff, M.E., Duggan, E., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-09-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2014-04-16
Changes: Experimental preparation - Version 1.3: 2017-10-25
Changes: Refinement description - Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary
