Download MendeleyCrystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3BA3
Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3BA3/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Lactiplantibacillus plantarum WCFS1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-11-07 Released: 2007-11-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 Å
- R-Value Free: 0.196
- R-Value Work: 0.170
- R-Value Observed: 0.171
wwPDB Validation 3D Report Full Report
This is version 1.5 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 |
| Pyridoxamine 5'-phosphate oxidase-like protein | 145 | Lactiplantibacillus plantarum WCFS1 | Mutation(s): 0 Gene Names: NP_783940.1, lp_0091 |  | |
UniProt | |||||
Find proteins for F9USS0 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9USS0 Go to UniProtKB: F9USS0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F9USS0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A], D [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| EDO Query on EDO | E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| 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: 1.55 Å
- R-Value Free: 0.196
- R-Value Work: 0.170
- R-Value Observed: 0.171
- Space Group: P 43 3 2
- Diffraction Data: https://doi.org/10.18430/M33BA3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 137.379 | α = 90 |
| b = 137.379 | β = 90 |
| c = 137.379 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| MOSFLM | data reduction |
Entry History
Deposition Data
- Released Date: 2007-11-20 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-11-20
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-01-25
Changes: Database references, Derived calculations - Version 1.5: 2024-10-09
Changes: Data collection, Structure summary
