Download MendeleyCrystal structure of putative aminotransferase (NP_107505.1) from Mesorhizobium loti at 1.55 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3GJU | pdb_00003gju
Crystal structure of a putative aminotransferase (mll7127) from mesorhizobium loti maff303099 at 1.55 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3GJU/pdb
- Classification: TRANSFERASE
- Organism(s): Mesorhizobium japonicum MAFF 303099
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2009-03-09 Released: 2009-03-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 Å
- R-Value Free: 0.168 (Depositor), 0.170 (DCC)
- R-Value Work: 0.139 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.140 (Depositor)
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 | 460 | Mesorhizobium japonicum MAFF 303099 | Mutation(s): 1 Gene Names: mll7127, NP_107505.1 |  | |
UniProt | |||||
Find proteins for Q987B2 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q987B2 Go to UniProtKB: Q987B2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q987B2 | ||||
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 |  | ||
| MPD Query on MPD | C [auth A], D [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-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: 1.55 Å
- R-Value Free: 0.168 (Depositor), 0.170 (DCC)
- R-Value Work: 0.139 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.140 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33GJU
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 113.224 | α = 90 |
| b = 59.577 | β = 130.59 |
| c = 85.337 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2009-03-17 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-03-17
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, 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
