Download MendeleyFlavoredoxin of Desulfovibrio vulgaris (Miyazaki F)
Ueda, Y., Shibata, N., Higuchi, Y.To be published.
2D5M | pdb_00002d5m
Flavoredoxin of Desulfovibrio vulgaris (Miyazaki F)
- PDB DOI: https://doi.org/10.2210/pdb2D5M/pdb
- Classification: ELECTRON TRANSPORT
- Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2005-11-02 Released: 2006-11-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.05 Å
- R-Value Free: 0.162 (Depositor), 0.160 (DCC)
- R-Value Work: 0.128 (Depositor), 0.130 (DCC)
- R-Value Observed: 0.135 (Depositor)
This is version 1.3 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 |
| flavoredoxin | 190 | Nitratidesulfovibrio vulgaris str. 'Miyazaki F | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for Q4W5X6 (Nitratidesulfovibrio vulgaris) Explore Q4W5X6 Go to UniProtKB: Q4W5X6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q4W5X6 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FMN Query on FMN | E [auth A] | FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N |  | ||
| MES Query on MES | F [auth A] | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | B [auth A], C [auth A], D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.05 Å
- R-Value Free: 0.162 (Depositor), 0.160 (DCC)
- R-Value Work: 0.128 (Depositor), 0.130 (DCC)
- R-Value Observed: 0.135 (Depositor)
Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.346 | α = 90 |
| b = 53.346 | β = 90 |
| c = 116.224 | γ = 120 |
| Software Name | Purpose |
|---|---|
| SHELX | model building |
| SHELXL-97 | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| SHELX | phasing |
Entry History
Deposition Data
- Released Date: 2006-11-21 Deposition Author(s): Ueda, Y., Shibata, N., Higuchi, Y.
Revision History (Full details and data files)
- Version 1.0: 2006-11-21
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations
