Download MendeleyCrystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633
Akazaki, H., Kawai, F., Kumaki, Y., Sekine, K., Hakamata, W., Nishio, T., Park, S.-Y., Oku, T.To be published.
2ZZS | pdb_00002zzs
2ZZS | pdb_00002zzs
Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633
- PDB DOI: https://doi.org/10.2210/pdb2ZZS/pdb
- Classification: ELECTRON TRANSPORT
- Organism(s): Vibrio parahaemolyticus RIMD 2210633
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-02-24 Released: 2010-03-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.242 (Depositor), 0.243 (DCC)
- R-Value Work: 0.193 (Depositor), 0.194 (DCC)
- R-Value Observed: 0.195 (Depositor)
Starting Model: experimental
View more details
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecule Content
- Total Structure Weight: 355.29 kDa
- Atom Count: 21,402
- Modeled Residue Count: 2,589
- Deposited Residue Count: 3,296
- Unique protein chains: 1
Macromolecules
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| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytochrome c554 | 103 | Vibrio parahaemolyticus RIMD 2210633 | Mutation(s): 0 Gene Names: VP2300 |  | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q87MF5 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEC Download:Ideal Coordinates CCD File | AB [auth R] CB [auth S] DB [auth T] EB [auth U] FB [auth V] | HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N |  | ||
| GOL Download:Ideal Coordinates CCD File | BB [auth R], JA [auth C], MA [auth E], YA [auth P] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.242 (Depositor), 0.243 (DCC)
- R-Value Work: 0.193 (Depositor), 0.194 (DCC)
- R-Value Observed: 0.195 (Depositor)
Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 84.949 | α = 71.5 |
| b = 87.612 | β = 72.98 |
| c = 103.847 | γ = 83.68 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2010-03-16 Deposition Author(s): Akazaki, H., Kawai, F., Kumaki, Y., Sekine, K., Hakamata, W., Nishio, T., Park, S.-Y., Oku, T.
Revision History (Full details and data files)
- Version 1.0: 2010-03-16
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2024-10-16
Changes: Structure summary
