Download MendeleyCrystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3KY8 | pdb_00003ky8
Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3KY8/pdb
- Classification: BIOSYNTHETIC PROTEIN
- Organism(s): Shewanella loihica PV-4
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-12-04 Released: 2009-12-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.12 Å
- R-Value Free: 0.231 (Depositor), 0.230 (DCC)
- R-Value Work: 0.181 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.184 (Depositor)
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 |
| Putative riboflavin biosynthesis protein | 197 | Shewanella loihica PV-4 | Mutation(s): 0 Gene Names: Shew_0776 |  | |
UniProt | |||||
Find proteins for A3QB00 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QB00 Go to UniProtKB: A3QB00 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A3QB00 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | E [auth A], J [auth B], K [auth B], L [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | F [auth A], G [auth A], M [auth B], N [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| UNL Query on UNL | C [auth A], D [auth A], H [auth B], I [auth B] | Unknown ligand 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: 2.12 Å
- R-Value Free: 0.231 (Depositor), 0.230 (DCC)
- R-Value Work: 0.181 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.184 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33KY8
Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.679 | α = 90 |
| b = 72.679 | β = 90 |
| c = 156.974 | 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: 2009-12-22 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-12-22
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description - Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-10-16
Changes: Data collection, Refinement description, Structure summary
