Download MendeleyThe crystal structure of xylulose kinase from Bifidobacterium adolescentis
Zhang, Z., Burley, S.K., Swaminathan, S.To be published.
3I8B
The crystal structure of xylulose kinase from Bifidobacterium adolescentis
- PDB DOI: https://doi.org/10.2210/pdb3I8B/pdb
- Classification: TRANSFERASE
- Organism(s): Bifidobacterium adolescentis ATCC 15703
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-07-09 Released: 2009-08-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.226
- R-Value Work: 0.180
- R-Value Observed: 0.183
wwPDB Validation 3D Report Full Report
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 |
| Xylulose kinase | 515 | Bifidobacterium adolescentis ATCC 15703 | Mutation(s): 0 Gene Names: xylB |  | |
UniProt | |||||
Find proteins for A1A0I0 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A1A0I0 Go to UniProtKB: A1A0I0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1A0I0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.00 Å
- R-Value Free: 0.226
- R-Value Work: 0.180
- R-Value Observed: 0.183
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 96.732 | α = 90 |
| b = 61.918 | β = 93.04 |
| c = 94.606 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| SOLVE | phasing |
| PHENIX | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2009-08-04 Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2009-08-04
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
