Download MendeleyCrystal structure of Putative Nitroreductase in Complex with FMN (YP_387283.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.70 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3E39 | pdb_00003e39
Crystal structure of a putative nitroreductase in complex with fmn (dde_0787) from desulfovibrio desulfuricans subsp. at 1.70 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3E39/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Oleidesulfovibrio alaskensis G20
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-08-06 Released: 2008-08-19
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.201 (Depositor), 0.200 (DCC)
- R-Value Work: 0.165 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.166 (Depositor)
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 Nitroreductase | 178 | Oleidesulfovibrio alaskensis G20 | Mutation(s): 0 Gene Names: YP_387283.1, Dde_0787 |  | |
UniProt | |||||
Find proteins for Q314Q8 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q314Q8 Go to UniProtKB: Q314Q8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q314Q8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FMN Query on FMN | E [auth A], G [auth B] | FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N |  | ||
| PGE Query on PGE | H [auth B] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | C [auth A], D [auth A], F [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-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: 1.70 Å
- R-Value Free: 0.201 (Depositor), 0.200 (DCC)
- R-Value Work: 0.165 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.166 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33E39
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 47.78 | α = 90 |
| b = 67.99 | β = 90 |
| c = 99.74 | 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: 2008-08-19 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-08-19
Type: Initial release - Version 1.1: 2011-07-13
Changes: 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: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, Structure summary
