Download MendeleyStructure of RC1339/APRc from Rickettsia conorii, a retropepsin-like aspartic protease
Li, M., Gustchina, A., Cruz, R., Simoes, M., Curto, P., Martinez, J., Faro, C., Simoes, I., Wlodawer, A.(2015) Acta Crystallogr D Biol Crystallogr 71: 2119-2126
5C9D | pdb_00005c9d
Crystal structure of a retropepsin-like aspartic protease from Rickettsia conorii
- PDB DOI: https://doi.org/10.2210/pdb5C9D/pdb
- Classification: HYDROLASE
- Organism(s): Rickettsia conorii
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-06-26 Released: 2015-10-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.59 Å
- R-Value Free: 0.298 (Depositor), 0.300 (DCC)
- R-Value Work: 0.227 (Depositor), 0.230 (DCC)
- R-Value Observed: 0.231 (Depositor)
wwPDB Validation 3D Report Full Report
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 |
| ApRick protease | 134 | Rickettsia conorii | Mutation(s): 0 Gene Names: RC1339 |  | |
UniProt | |||||
Find proteins for Q92FY8 (Rickettsia conorii (strain ATCC VR-613 / Malish 7)) Explore Q92FY8 Go to UniProtKB: Q92FY8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q92FY8 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NA Query on NA | C [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.59 Å
- R-Value Free: 0.298 (Depositor), 0.300 (DCC)
- R-Value Work: 0.227 (Depositor), 0.230 (DCC)
- R-Value Observed: 0.231 (Depositor)
Space Group: I 41 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 105.29 | α = 90 |
| b = 105.29 | β = 90 |
| c = 90.996 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2015-10-14 Deposition Author(s): Li, M., Gustchina, A., Cruz, R., Simoes, M., Curto, P., Martinez, J., Faro, C., Simoes, I., Wlodawer, A.
Revision History (Full details and data files)
- Version 1.0: 2015-10-14
Type: Initial release - Version 2.0: 2018-03-14
Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary - Version 2.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations
