Download MendeleyCrystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776
Chang, C., Gu, M., Endres, M., Joachimiak, A.To be published.
4OVY
Crystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776
- PDB DOI: https://doi.org/10.2210/pdb4OVY/pdb
- Classification: HYDROLASE
- Organism(s): Planctopirus limnophila DSM 3776
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-01-24 Released: 2014-02-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.175
- R-Value Work: 0.131
- R-Value Observed: 0.133
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Haloacid dehalogenase domain protein hydrolase | 310 | Planctopirus limnophila DSM 3776 | Mutation(s): 0 Gene Names: Plim_1241 |  | |
UniProt | |||||
Find proteins for D5SUM3 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SUM3 Go to UniProtKB: D5SUM3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D5SUM3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CIT Query on CIT | B [auth A], C [auth A] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | J [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | 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: 0.175
- R-Value Work: 0.131
- R-Value Observed: 0.133
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.95 | α = 90 |
| b = 75.502 | β = 90 |
| c = 64.357 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2014-02-05 Deposition Author(s): Chang, C., Gu, M., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2014-02-05
Type: Initial release - Version 1.1: 2015-02-25
Changes: Derived calculations - Version 1.2: 2017-11-22
Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy - Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description
