Download MendeleyDye-decolorizing peroxidase (DyP) complex with ascorbic acid
Sugano, Y., Yoshida, T., Tsuge, H.To be published.
3VXI | pdb_00003vxi
Dye-decolorizing peroxidase (DyP) complex with ascorbic acid
- PDB DOI: https://doi.org/10.2210/pdb3VXI/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Bjerkandera adusta
- Expression System: Aspergillus oryzae
- Mutation(s): No
- Deposited: 2012-09-14 Released: 2012-11-07
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.193 (Depositor), 0.200 (DCC)
- R-Value Work: 0.173 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.174 (Depositor)
Starting Model: experimental
View more details
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 |
| DyP | 442 | Bjerkandera adusta | Mutation(s): 0 Gene Names: dyp EC: 1.11.1.19 |  | |
UniProt | |||||
Find proteins for Q8WZK8 (Bjerkandera adusta) Explore Q8WZK8 Go to UniProtKB: Q8WZK8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8WZK8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEM Query on HEM | B [auth A] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L |  | ||
| ASC Query on ASC | C [auth A] | ASCORBIC ACID C6 H8 O6 CIWBSHSKHKDKBQ-JLAZNSOCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.193 (Depositor), 0.200 (DCC)
- R-Value Work: 0.173 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.174 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 46.892 | α = 90 |
| b = 95.912 | β = 103.81 |
| c = 50.333 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2012-11-07 Deposition Author(s): Sugano, Y., Yoshida, T., Tsuge, H.
Revision History (Full details and data files)
- Version 1.0: 2012-11-07
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description - 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
