Download MendeleyCrystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3EJK
Crystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3EJK/pdb
- Classification: ISOMERASE
- Organism(s): Oleidesulfovibrio alaskensis G20
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-09-18 Released: 2008-09-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.217
- R-Value Work: 0.169
- R-Value Observed: 0.171
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 |
| dTDP Sugar Isomerase | 174 | Oleidesulfovibrio alaskensis G20 | Mutation(s): 0 Gene Names: YP_390184.1, Dde_3696 |  | |
UniProt | |||||
Find proteins for Q30V07 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q30V07 Go to UniProtKB: Q30V07 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q30V07 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Query on PG4 | E [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| CIT Query on CIT | C [auth A], D [auth A] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | F [auth A], G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| UNL Query on UNL | B [auth A] | Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
| 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: 1.95 Å
- R-Value Free: 0.217
- R-Value Work: 0.169
- R-Value Observed: 0.171
- Space Group: C 2 2 21
- Diffraction Data: https://doi.org/10.18430/M33EJK
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 81.79 | α = 90 |
| b = 86.51 | β = 90 |
| c = 51.34 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2008-09-30 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-09-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, 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
