Download MendeleyCrystal structure of Putative carboxypeptidase A (YP_562911.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.39 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3L2N
Crystal structure of Putative carboxypeptidase A (YP_562911.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.39 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3L2N/pdb
- Classification: HYDROLASE
- Organism(s): Shewanella denitrificans OS217
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-12-15 Released: 2009-12-29
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.39 Å
- R-Value Free: 0.233
- R-Value Work: 0.180
- R-Value Observed: 0.182
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 M14, carboxypeptidase A | 395 | Shewanella denitrificans OS217 | Mutation(s): 0 Gene Names: Sden_1905 |  | |
UniProt | |||||
Find proteins for Q12MY8 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12MY8 Go to UniProtKB: Q12MY8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q12MY8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | I [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | E [auth A], F [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| CA Query on CA | C [auth A], G [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| UNL Query on UNL | D [auth A], H [auth B] | Unknown ligand BHPQYMZQTOCNFJ-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: 2.39 Å
- R-Value Free: 0.233
- R-Value Work: 0.180
- R-Value Observed: 0.182
- Space Group: P 61 2 2
- Diffraction Data: https://doi.org/10.18430/M33L2N
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 81.417 | α = 90 |
| b = 81.417 | β = 90 |
| c = 479.685 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2009-12-29 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-12-29
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description - Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
