Download MendeleyCrystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio desulfuricans G20 at 1.60 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
2RB7
Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio desulfuricans G20 at 1.60 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2RB7/pdb
- Classification: HYDROLASE
- Organism(s): Oleidesulfovibrio alaskensis G20
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-09-18 Released: 2007-10-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.180
- R-Value Work: 0.154
- R-Value Observed: 0.155
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 |
| Peptidase, M20/M25/M40 family | 364 | Oleidesulfovibrio alaskensis G20 | Mutation(s): 0 Gene Names: YP_387682.1, Dde_1186 |  | |
UniProt | |||||
Find proteins for Q313A9 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q313A9 Go to UniProtKB: Q313A9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q313A9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Query on PG4 | E [auth B] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PGE Query on PGE | C [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | D [auth A], F [auth B], G [auth B], H [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-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: 1.60 Å
- R-Value Free: 0.180
- R-Value Work: 0.154
- R-Value Observed: 0.155
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M32RB7
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.85 | α = 90 |
| b = 82.19 | β = 91.37 |
| c = 89.34 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2007-10-02 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-10-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-01-25
Changes: Database references
