Download MendeleyThe crystal structure of xylulose kinase from Lactobacillus acidophilus
Zhang, Z., Burley, S.K., Swaminathan, S.To be published.
3LL3
The crystal structure of ligand bound xylulose kinase from Lactobacillus acidophilus
- PDB DOI: https://doi.org/10.2210/pdb3LL3/pdb
- Classification: TRANSFERASE
- Organism(s): Lactobacillus acidophilus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-01-28 Released: 2010-03-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.224
- R-Value Work: 0.196
- R-Value Observed: 0.197
Starting Model: experimental
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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 |
| Gluconate kinase | 504 | Lactobacillus acidophilus | Mutation(s): 0 Gene Names: LBA0354 EC: 2.7.1.12 |  | |
UniProt | |||||
Find proteins for Q5FM28 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FM28 Go to UniProtKB: Q5FM28 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5FM28 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | C [auth A] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| ADP Query on ADP | F [auth B] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N |  | ||
| DXP Query on DXP | D [auth A], G [auth B] | 1-DEOXY-D-XYLULOSE-5-PHOSPHATE C5 H11 O7 P AJPADPZSRRUGHI-RFZPGFLSSA-N |  | ||
| XUL Query on XUL | E [auth A] | D-XYLULOSE C5 H10 O5 ZAQJHHRNXZUBTE-WUJLRWPWSA-N |  | ||
| 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: 2.00 Å
- R-Value Free: 0.224
- R-Value Work: 0.196
- R-Value Observed: 0.197
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.889 | α = 84.75 |
| b = 73.056 | β = 86.32 |
| c = 82.872 | γ = 77.95 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| PHASER | phasing |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2010-03-23 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: 2010-03-23
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 - Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description - Version 1.4: 2023-11-22
Changes: Data collection
