Download MendeleyCrystal structure of putative aminotransferase (YP_614685.1) from SILICIBACTER SP. TM1040 at 1.80 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3FCR
Crystal structure of putative aminotransferase (YP_614685.1) from SILICIBACTER SP. TM1040 at 1.80 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3FCR/pdb
- Classification: TRANSFERASE
- Organism(s): Ruegeria sp. TM1040
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2008-11-22 Released: 2009-01-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.254
- R-Value Work: 0.205
- R-Value Observed: 0.208
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 aminotransferase | 458 | Ruegeria sp. TM1040 | Mutation(s): 1 Gene Names: TM1040_2691, YP_614685.1 EC: 2.6.1 |  | |
UniProt | |||||
Find proteins for Q1GD43 (Ruegeria sp. (strain TM1040)) Explore Q1GD43 Go to UniProtKB: Q1GD43 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q1GD43 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PLP Query on PLP | B [auth A] | PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | C [auth A], D [auth A], E [auth A], F [auth A], G [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | A | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.254
- R-Value Work: 0.205
- R-Value Observed: 0.208
- Space Group: C 1 2 1
- Diffraction Data: https://doi.org/10.18430/M33FCR
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 76.85 | α = 90 |
| b = 96.25 | β = 105.51 |
| c = 60.3 | γ = 90 |
| 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: 2009-01-13 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-01-13
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
