Download MendeleyThe Crystal Structure of the Creatinase/Prolidase N-terminal domain of an X-PRO dipeptidase from Streptococcus pyogenes to 1.85A
Stein, A.J., Wu, R., Clancy, S., Joachimiak, A.To be published.
3O5V | pdb_00003o5v
The Crystal Structure of the Creatinase/Prolidase N-terminal domain of an X-PRO dipeptidase from Streptococcus pyogenes to 1.85A
- PDB DOI: https://doi.org/10.2210/pdb3O5V/pdb
- Classification: HYDROLASE
- Organism(s): Streptococcus pyogenes M1 GAS
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-07-28 Released: 2010-08-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.224 (Depositor), 0.226 (DCC)
- R-Value Work: 0.192 (Depositor), 0.192 (DCC)
- R-Value Observed: 0.194 (Depositor)
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 |
| X-PRO dipeptidase | 132 | Streptococcus pyogenes M1 GAS | Mutation(s): 0 Gene Names: M5005_Spy0423, pepQ, SPy_0513 EC: 3.4.13.9 |  | |
UniProt | |||||
Find proteins for Q9A119 (Streptococcus pyogenes serotype M1) Explore Q9A119 Go to UniProtKB: Q9A119 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9A119 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-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: 1.85 Å
- R-Value Free: 0.224 (Depositor), 0.226 (DCC)
- R-Value Work: 0.192 (Depositor), 0.192 (DCC)
- R-Value Observed: 0.194 (Depositor)
Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 79.439 | α = 90 |
| b = 79.439 | β = 90 |
| c = 88.823 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELX | phasing |
| MLPHARE | phasing |
| DM | phasing |
| ARP/wARP | model building |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2010-08-11 Deposition Author(s): Stein, A.J., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2010-08-11
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-08
Changes: Refinement description - Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary
