Download MendeleyCrystal structure of xylitol-bound glucose isomerase by serial millisecond crystallography
Nam, K.H.To be published.
7DFK
Crystal structure of xylitol-bound glucose isomerase by serial millisecond crystallography
- PDB DOI: https://doi.org/10.2210/pdb7DFK/pdb
- Classification: ISOMERASE
- Organism(s): Streptomyces rubiginosus
- Mutation(s): No
- Deposited: 2020-11-08 Released: 2021-11-17
- Funding Organization(s): National Research Foundation (NRF, Korea)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 ?
- R-Value Free: 0.251
- R-Value Work: 0.235
- R-Value Observed: 0.235
Starting Model: experimental
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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 |
| Xylose isomerase | 388 | Streptomyces rubiginosus | Mutation(s): 0 EC: 5.3.1.5 |  | |
UniProt | |||||
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300 Go to UniProtKB: P24300 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P24300 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| XYL (Subject of Investigation/LOI) Query on XYL | C [auth A] | Xylitol C5 H12 O5 HEBKCHPVOIAQTA-SCDXWVJYSA-N |  | ||
| MG (Subject of Investigation/LOI) Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 ?
- R-Value Free: 0.251
- R-Value Work: 0.235
- R-Value Observed: 0.235
- Space Group: I 2 2 2
- Diffraction Data: https://doi.org/10.11577/1777828
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 94.138 | ¦Á = 90 |
| b = 99.936 | ¦Â = 90 |
| c = 103.156 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-11-17 Deposition Author(s): Nam, K.H.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Research Foundation (NRF, Korea) | Korea, Republic Of | NRF-2017M3A9F6029736 |
| National Research Foundation (NRF, Korea) | Korea, Republic Of | NRF-2017R1D1A1B03033087 |
Revision History (Full details and data files)
- Version 1.0: 2021-11-17
Type: Initial release - Version 1.1: 2023-09-06
Changes: Data collection, Database references - Version 1.2: 2023-11-29
Changes: Refinement description
