Download MendeleyHydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde prepared by cocrystallization
Nuylert, A., Nakabayashi, M., Yamaguchi, T., Asano, Y.To be published.
7BR1
Hydroxynitrile lyase from Parafontaria laminate complexed with benzaldehyde prepared by cocrystallization
- PDB DOI: https://doi.org/10.2210/pdb7BR1/pdb
- Classification: LYASE
- Organism(s): Parafontaria laminata
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2020-03-26 Released: 2021-04-07
- Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 ?
- R-Value Free: 0.147
- R-Value Work: 0.140
- R-Value Observed: 0.141
Starting Model: experimental
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This is version 1.3 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 |
| Hydroxynitrile lyase | 164 | Parafontaria laminata | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for A0A7I6N400 (Parafontaria laminata) Explore A0A7I6N400 Go to UniProtKB: A0A7I6N400 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A7I6N400 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HBX (Subject of Investigation/LOI) Query on HBX | C [auth A], D [auth A], H [auth B], I [auth B] | benzaldehyde C7 H6 O HUMNYLRZRPPJDN-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | G [auth A], L [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| SCN (Subject of Investigation/LOI) Query on SCN | E [auth A], F [auth A], J [auth B], K [auth B] | THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 ?
- R-Value Free: 0.147
- R-Value Work: 0.140
- R-Value Observed: 0.141
- Space Group: P 1 21 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 56.934 | ¦Á = 90 |
| b = 32.763 | ¦Â = 102.84 |
| c = 84.632 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-04-07 Deposition Author(s): Nuylert, A., Nakabayashi, M., Yamaguchi, T., Asano, Y.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Science and Technology | Japan | JPMJER1102 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 17H06169 |
Revision History (Full details and data files)
- Version 1.0: 2021-04-07
Type: Initial release - Version 1.1: 2021-07-28
Changes: Source and taxonomy, Structure summary - Version 1.2: 2023-11-29
Changes: Data collection, Database references, Refinement description - Version 1.3: 2024-11-20
Changes: Structure summary
