Download MendeleyCrystal structure of putative thioesterase (YP_614486.1) from Silicibacter sp. TM1040 at 1.79 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
2PBL
Crystal structure of a putative thioesterase (tm1040_2492) from silicibacter sp. tm1040 at 1.79 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2PBL/pdb
- Classification: HYDROLASE
- Organism(s): Ruegeria sp. TM1040
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-03-28 Released: 2007-04-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.79 Å
- R-Value Free: 0.270
- R-Value Work: 0.221
- R-Value Observed: 0.224
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 |
| Putative esterase/lipase/thioesterase | A, B, C, D | 262 | Ruegeria sp. TM1040 | Mutation(s): 7 Gene Names: YP_614486.1, TM1040_2492 |  |
UniProt | |||||
Find proteins for Q1GDP2 (Ruegeria sp. (strain TM1040)) Explore Q1GDP2 Go to UniProtKB: Q1GDP2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q1GDP2 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | I [auth B], L [auth C] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | Ligand Interaction | |
| CL Query on CL | E [auth A], H [auth B], K [auth C], N [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| MG Query on MG | G [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
| UNL Query on UNL | F [auth A], J [auth B], M [auth C], O [auth D] | Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N | Ligand Interaction | ||
| 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: 1.79 Å
- R-Value Free: 0.270
- R-Value Work: 0.221
- R-Value Observed: 0.224
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M32PBL
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 77.197 | α = 90 |
| b = 74.438 | β = 113.39 |
| c = 95.727 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| SHELX | phasing |
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2007-04-17 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-04-17
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
