Download MendeleyCrystal Structure of a Phosphoserine phosphatase (SerB) from Helicobacter pylori
Syed Ibrahim, B., Burley, S.K., Swaminathan, S.To be published.
3M1Y
Crystal Structure of a Phosphoserine phosphatase (SerB) from Helicobacter pylori
- PDB DOI: https://doi.org/10.2210/pdb3M1Y/pdb
- Classification: HYDROLASE
- Organism(s): Helicobacter pylori
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-03-05 Released: 2010-03-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.271
- R-Value Work: 0.229
- R-Value Observed: 0.229
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Phosphoserine phosphatase (SerB) | 217 | Helicobacter pylori | Mutation(s): 0 Gene Names: HP_0652 |  | |
UniProt | |||||
Find proteins for O25367 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25367 Go to UniProtKB: O25367 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O25367 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CL Query on CL | F [auth A], G [auth A], I [auth B], K [auth C], N [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | E [auth A], H [auth B], J [auth C], L [auth C], M [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.271
- R-Value Work: 0.229
- R-Value Observed: 0.229
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.607 | α = 90 |
| b = 84.719 | β = 90 |
| c = 204.826 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| SHELX | model building |
| SHARP | phasing |
| CNS | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| SHELX | phasing |
Entry History
Deposition Data
- Released Date: 2010-03-23 Deposition Author(s): Syed Ibrahim, B., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2010-03-23
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
