Download MendeleyCrystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri
Kim, Y., Mack, J., Buck, K., Joachimiak, A.To be published.
3NKL
Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri
- PDB DOI: https://doi.org/10.2210/pdb3NKL/pdb
- Classification: oxidoreductase/lyase
- Organism(s): Aliivibrio fischeri ES114
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2010-06-20 Released: 2010-08-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.195
- R-Value Work: 0.167
- R-Value Observed: 0.169
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| UDP-D-quinovosamine 4-dehydrogenase | 141 | Aliivibrio fischeri ES114 | Mutation(s): 0 Gene Names: VF_0197 EC: 1.1.1 (PDB Primary Data), 4.2.1 (PDB Primary Data) |  | |
UniProt | |||||
Find proteins for Q5E8F4 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5E8F4 Go to UniProtKB: Q5E8F4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5E8F4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A], E [auth A], G [auth A], J [auth B], K [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | D [auth A], H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACY Query on ACY | F [auth A] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| CL Query on CL | I [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| 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: 1.90 Å
- R-Value Free: 0.195
- R-Value Work: 0.167
- R-Value Observed: 0.169
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 108.262 | α = 90 |
| b = 45.379 | β = 91.54 |
| c = 69.813 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| SHELXS | phasing |
| MLPHARE | phasing |
| BUCCANEER | model building |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| BUCCANEER | phasing |
Entry History
Deposition Data
- Released Date: 2010-08-18 Deposition Author(s): Kim, Y., Mack, J., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2010-08-18
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary
