Download MendeleyCrystal structure of pyridoxamine 5'-phosphate oxidase-related FMN-binding (YP_508196.1) from Jannaschia sp. CCS1 at 1.60 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
2OU5
Crystal structure of a pyridoxamine 5'-phosphate oxidase-related fmn-binding protein (jann_0254) from jannaschia sp. ccs1 at 1.60 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2OU5/pdb
- Classification: FLAVOPROTEIN
- Organism(s): Jannaschia sp. CCS1
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-02-09 Released: 2007-03-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.221
- R-Value Work: 0.178
- R-Value Observed: 0.181
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 |
| Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | 175 | Jannaschia sp. CCS1 | Mutation(s): 2 Gene Names: YP_508196.1, Jann_0254 |  | |
UniProt | |||||
Find proteins for Q28VU1 (Jannaschia sp. (strain CCS1)) Explore Q28VU1 Go to UniProtKB: Q28VU1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q28VU1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FMN Query on FMN | D [auth A], F [auth B] | FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N |  | ||
| SO4 Query on SO4 | C [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | E [auth A], G [auth B], H [auth B], I [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.60 Å
- R-Value Free: 0.221
- R-Value Work: 0.178
- R-Value Observed: 0.181
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M32OU5
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 45.88 | α = 90 |
| b = 68.51 | β = 90 |
| c = 111.92 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| SHELX | phasing |
| REFMAC | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| XDS | data reduction |
| SHELXD | phasing |
| SHARP | phasing |
Entry History
Deposition Data
- Released Date: 2007-03-06 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-03-06
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, 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
