Download MendeleyThe Crystal Structure of a Short-chain Dehydrogenase from Streptomyces avermitilis to 2A
Stein, A.J., Evdokimova, E., Egorova, O., Savchenko, A., Joachimiak, A.To be published.
3M1A | pdb_00003m1a
The Crystal Structure of a Short-chain Dehydrogenase from Streptomyces avermitilis to 2A
- PDB DOI: https://doi.org/10.2210/pdb3M1A/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Streptomyces avermitilis
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2010-03-04 Released: 2010-03-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.242 (Depositor), 0.240 (DCC)
- R-Value Work: 0.197 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.200 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.4 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 dehydrogenase | 281 | Streptomyces avermitilis | Mutation(s): 1 Gene Names: SAV770, SAV_770 |  | |
UniProt | |||||
Find proteins for Q82PV2 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82PV2 Go to UniProtKB: Q82PV2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q82PV2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACT Query on ACT | O [auth E], P [auth I] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| NA Query on NA | K [auth A], L [auth B], M [auth D], N [auth E] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D, E A, B, C, D, E, F, G, H, I, J | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.242 (Depositor), 0.240 (DCC)
- R-Value Work: 0.197 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.200 (Depositor)
Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 136.638 | α = 90 |
| b = 202.779 | β = 90 |
| c = 106.339 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| SHELX | phasing |
| DM | phasing |
| BUCCANEER | phasing |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2010-03-23 Deposition Author(s): Stein, A.J., Evdokimova, E., Egorova, O., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2010-03-23
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-08
Changes: Refinement description - Version 1.3: 2021-10-13
Changes: Database references, Derived calculations - Version 1.4: 2024-11-20
Changes: Data collection, Structure summary
