Download MendeleyDomain-swapped cytochrome cb562 dimer and its nanocage encapsulating a Zn-SO4 cluster in the internal cavity
Miyamoto, T., Kuribayashi, M., Nagao, S., Shomura, Y., Higuchi, Y., Hirota, S.(2015) Chem Sci
5AWI
Domain-swapped cytochrome cb562 dimer
- PDB DOI: https://doi.org/10.2210/pdb5AWI/pdb
- Classification: ELECTRON TRANSPORT
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2015-07-03 Released: 2015-10-21
- Funding Organization(s): JSPS
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.205
- R-Value Work: 0.180
- R-Value Observed: 0.181
This is version 2.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Soluble cytochrome b562 | 106 | Escherichia coli | Mutation(s): 2 Gene Names: cybC |  | |
UniProt | |||||
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0ABE7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEC Query on HEC | C [auth A], J [auth A] | HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N |  | ||
| SO4 Query on SO4 | H [auth A], I [auth A], N [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ZN Query on ZN | D [auth A] E [auth A] F [auth A] G [auth A] K [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.205
- R-Value Work: 0.180
- R-Value Observed: 0.181
- Space Group: P 21 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 94.608 | α = 90 |
| b = 94.608 | β = 90 |
| c = 94.608 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-10-21 Deposition Author(s): Miyamoto, T., Kuribayashi, M., Nagao, S., Shomura, Y., Higuchi, Y., Hirota, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| JSPS | Japan | 26288080 |
| JSPS | Japan | 15K13744 |
Revision History (Full details and data files)
- Version 1.0: 2015-10-21
Type: Initial release - Version 2.0: 2019-10-02
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
