Download MendeleyCrystal structure of uncharacterized peroxidase-related protein (YP_614459.1) from Silicibacter sp. TM1040 at 1.70 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
2PFX
Crystal structure of uncharacterized peroxidase-related protein (YP_614459.1) from Silicibacter sp. TM1040 at 1.70 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2PFX/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Ruegeria sp. TM1040
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-04-05 Released: 2007-04-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 ?
- R-Value Free: 0.165
- R-Value Observed: 0.114
wwPDB Validation 3D Report Full Report
This is version 1.6 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 |
| Uncharacterized peroxidase-related protein | 191 | Ruegeria sp. TM1040 | Mutation(s): 13 Gene Names: YP_614459.1, TM1040_2465 |  | |
UniProt | |||||
Find proteins for Q1GDR9 (Ruegeria sp. (strain TM1040)) Explore Q1GDR9 Go to UniProtKB: Q1GDR9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q1GDR9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Query on PG4 | D [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | C [auth A], E [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| CL Query on CL | F [auth B] | 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: 1.70 ?
- R-Value Free: 0.165
- R-Value Observed: 0.114
- Space Group: P 63
- Diffraction Data: https://doi.org/10.18430/M32PFX
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 85.069 | ¦Á = 90 |
| b = 85.069 | ¦Â = 90 |
| c = 105.616 | ¦Ă = 120 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| SHELX | phasing |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| SHELXD | phasing |
| SOLVE | phasing |
| SHELXL-97 | refinement |
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: Derived calculations, Source and taxonomy, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2017-10-25
Changes: Author supporting evidence - Version 1.5: 2023-01-25
Changes: Database references, Derived calculations - Version 1.6: 2024-11-06
Changes: Data collection, Structure summary
