Download MendeleyHydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde
Nuylert, A., Nakabayashi, M., Yamaguchi, T., Asano, Y.To be published.
7BPO
Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde
- PDB DOI: https://doi.org/10.2210/pdb7BPO/pdb
- Classification: LYASE
- Organism(s): Parafontaria falcifera
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2020-03-23 Released: 2021-03-24
- Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.37 ?
- R-Value Free: 0.176
- R-Value Work: 0.159
- R-Value Observed: 0.160
Starting Model: experimental
View more details
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 |
| Hydroxynitrile lyase | 165 | Parafontaria falcifera | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HBX (Subject of Investigation/LOI) Query on HBX | C [auth A], E [auth B] | benzaldehyde C7 H6 O HUMNYLRZRPPJDN-UHFFFAOYSA-N |  | ||
| GOL (Subject of Investigation/LOI) Query on GOL | D [auth A], F [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.37 ?
- R-Value Free: 0.176
- R-Value Work: 0.159
- R-Value Observed: 0.160
- Space Group: P 1 21 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 68.304 | ¦Á = 90 |
| b = 33.13 | ¦Â = 106.17 |
| c = 72.018 | ¦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: 2021-03-24 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: 2021-03-24
Type: Initial release - Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description - Version 1.2: 2024-10-16
Changes: Structure summary
