Download MendeleyCrystal structure of putative nitroreductase in complex with FMN (YP_001089721.1) from CLOSTRIDIUM DIFFICILE 630 at 1.35 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3GFA
Crystal structure of a putative nitroreductase in complex with fmn (cd3205) from clostridium difficile 630 at 1.35 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3GFA/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Clostridioides difficile 630
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-02-26 Released: 2009-03-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.157
- R-Value Work: 0.134
- R-Value Observed: 0.135
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 | 198 | Clostridioides difficile 630 | Mutation(s): 0 Gene Names: CD3205, YP_001089721.1 |  | |
UniProt | |||||
Find proteins for Q17ZU8 (Clostridioides difficile (strain 630)) Explore Q17ZU8 Go to UniProtKB: Q17ZU8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q17ZU8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FMN Query on FMN | C [auth A], H [auth B] | FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N |  | ||
| MRD Query on MRD | K [auth B] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N |  | ||
| MPD Query on MPD | J [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| GOL Query on GOL | E [auth A], F [auth A], G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A], 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: 1.35 Å
- R-Value Free: 0.157
- R-Value Work: 0.134
- R-Value Observed: 0.135
- Space Group: C 1 2 1
- Diffraction Data: https://doi.org/10.18430/M33GFA
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 73.336 | α = 90 |
| b = 109.891 | β = 104.84 |
| c = 60.635 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
Entry History
Deposition Data
- Released Date: 2009-03-17 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-03-17
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2017-10-25
Changes: Author supporting evidence, 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: 2024-10-16
Changes: Data collection, Structure summary
