Download MendeleyCrystal structure of an Iron-containing alcohol dehydrogenase (Sden_2133) from Shewanella denitrificans OS-217 at 2.12 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3RF7
Crystal structure of an Iron-containing alcohol dehydrogenase (Sden_2133) from Shewanella denitrificans OS-217 at 2.12 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3RF7/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Shewanella denitrificans OS217
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-04-05 Released: 2011-12-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.12 Å
- R-Value Free: 0.197
- R-Value Work: 0.182
- R-Value Observed: 0.183
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 |
| Iron-containing alcohol dehydrogenase | 375 | Shewanella denitrificans OS217 | Mutation(s): 0 Gene Names: Sden_2133 |  | |
UniProt | |||||
Find proteins for Q12MB1 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12MB1 Go to UniProtKB: Q12MB1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q12MB1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 8 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAD Query on NAD | C [auth A] | NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N |  | ||
| EPE Query on EPE | D [auth A] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | M [auth A], N [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| NI Query on NI | F [auth A] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
| FE Query on FE | E [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| CA Query on CA | K [auth A], L [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | G [auth A], H [auth A], I [auth A], J [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| UNL Query on UNL | B [auth A] | Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | 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: 0.197
- R-Value Work: 0.182
- R-Value Observed: 0.183
- Space Group: I 41 2 2
- Diffraction Data: https://doi.org/10.18430/M33RF7
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 121.074 | α = 90 |
| b = 121.074 | β = 90 |
| c = 275.666 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| PDB_EXTRACT | data extraction |
| SHELX | phasing |
| SHARP | phasing |
| SCALA | data scaling |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SHELXD | phasing |
Entry History
Deposition Data
- Released Date: 2011-12-07 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2011-12-07
Type: Initial release - Version 1.1: 2017-10-25
Changes: Author supporting evidence, Refinement description - Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary
