5J8L
Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy L-tagatose, using a crystal grown in microgravity
- PDB DOI: https://doi.org/10.2210/pdb5J8L/pdb
- Entry: 5J8L supersedes: 4YVL
- Classification: ISOMERASE
- Organism(s): Pseudomonas cichorii
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2016-04-08 Released: 2016-04-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.73 Å
- R-Value Free: 0.219
- R-Value Work: 0.194
- R-Value Observed: 0.197
This is version 1.3 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| D-tagatose 3-epimerase | 300 | Pseudomonas cichorii | Mutation(s): 1 EC: 5.1.3.31 |  | |
UniProt | |||||
Find proteins for O50580 (Pseudomonas cichorii) Explore O50580 Go to UniProtKB: O50580 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O50580 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TGK Query on TGK | H [auth A] I [auth A] K [auth B] L [auth B] N [auth C] | 1-deoxy-beta-L-tagatopyranose C6 H12 O5 YLWWLYACYNLGLT-KCDKBNATSA-N |  | ||
| TGJ Query on TGJ | F [auth A], G [auth A] | 1-deoxy-L-tagatose C6 H12 O5 IXDZFGATLNCIOI-HCWXCVPCSA-N |  | ||
| MN Query on MN | E [auth A], J [auth B], M [auth C], P [auth D] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.73 Å
- R-Value Free: 0.219
- R-Value Work: 0.194
- R-Value Observed: 0.197
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 52.58 | α = 90 |
| b = 126.535 | β = 101.45 |
| c = 98.903 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2016-04-27 Deposition Author(s): Yoshida, H., Yoshihara, A., Izumori, K., Kamitori, S.
- This entry supersedes: 4YVL
Revision History (Full details and data files)
- Version 1.0: 2016-04-27
Type: Initial release - Version 1.1: 2017-12-13
Changes: Data collection, Database references, Derived calculations - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations - Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
