Download MendeleyCrystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9 solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).
Suzuki, K., Koitabashi, M.To be published.
7CY9 | pdb_00007cy9
Crystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9 solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).
- PDB DOI: https://doi.org/10.2210/pdb7CY9/pdb
- Classification: HYDROLASE
- Organism(s): Paraphoma sp. B47-9
- Mutation(s): No
- Deposited: 2020-09-03 Released: 2020-09-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.36 Å
- R-Value Free: 0.166 (Depositor), 0.170 (DCC)
- R-Value Work: 0.122 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.124 (Depositor)
This is version 2.1 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 |
| Cutinase | 195 | Paraphoma sp. B47-9 | Mutation(s): 0 EC: 3.1.1.74 |  | |
UniProt | |||||
Find proteins for A0A060N399 (Paraphoma sp. B47-9) Explore A0A060N399 Go to UniProtKB: A0A060N399 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A060N399 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CAD (Subject of Investigation/LOI) Query on CAD | C [auth A], D [auth A], G [auth B] | CACODYLIC ACID C2 H7 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-N |  | ||
| NA Query on NA | E [auth A], F [auth A], H [auth B], I [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PCA Query on PCA | A, B | L-PEPTIDE LINKING | C5 H7 N O3 |  | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.36 Å
- R-Value Free: 0.166 (Depositor), 0.170 (DCC)
- R-Value Work: 0.122 (Depositor), 0.120 (DCC)
- R-Value Observed: 0.124 (Depositor)
Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 34.886 | α = 103.78 |
| b = 43.517 | β = 92.42 |
| c = 51.724 | γ = 101.49 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| Aimless | data scaling |
| SHELX | phasing |
| PDB_EXTRACT | data extraction |
| xia2 | data reduction |
Entry History
Deposition Data
- Released Date: 2020-09-30 Deposition Author(s): Suzuki, K., Koitabashi, M.
Revision History (Full details and data files)
- Version 1.0: 2020-09-30
Type: Initial release - Version 2.0: 2020-12-16
Type: Coordinate replacement
Reason: Model orientation/position
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary - Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary
