Download MendeleyCrystal structure of urease from Yersinia enterocolitica
Studer, G., Jakob, R.P., Mahi, M.A., Wiesand, U., Schwede, T., Maier, T.To be published.
4Z42
Crystal structure of urease from Yersinia enterocolitica
- PDB DOI: https://doi.org/10.2210/pdb4Z42/pdb
- Classification: HYDROLASE
- Organism(s): Yersinia enterocolitica W22703
- Mutation(s): No
- Deposited: 2015-04-01 Released: 2016-04-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.01 Å
- R-Value Free: 0.298
- R-Value Work: 0.277
- R-Value Observed: 0.278
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Urease subunit gamma | 100 | Yersinia enterocolitica W22703 | Mutation(s): 0 EC: 3.5.1.5 |  | |
UniProt | |||||
Find proteins for F4MWM9 (Yersinia enterocolitica W22703) Explore F4MWM9 Go to UniProtKB: F4MWM9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F4MWM9 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Urease subunit beta | 164 | Yersinia enterocolitica W22703 | Mutation(s): 0 EC: 3.5.1.5 |  | |
UniProt | |||||
Find proteins for F4MWM8 (Yersinia enterocolitica W22703) Explore F4MWM8 Go to UniProtKB: F4MWM8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F4MWM8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Urease subunit alpha | 572 | Yersinia enterocolitica W22703 | Mutation(s): 0 EC: 3.5.1.5 |  | |
UniProt | |||||
Find proteins for F4MWM7 (Yersinia enterocolitica W22703) Explore F4MWM7 Go to UniProtKB: F4MWM7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F4MWM7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NI Query on NI | M [auth C] N [auth C] O [auth F] P [auth F] Q [auth I] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.01 Å
- R-Value Free: 0.298
- R-Value Work: 0.277
- R-Value Observed: 0.278
- Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 157.2 | α = 90 |
| b = 157.2 | β = 90 |
| c = 774.62 | γ = 120 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2016-04-13 Deposition Author(s): Studer, G., Jakob, R.P., Mahi, M.A., Wiesand, U., Schwede, T., Maier, T.
Revision History (Full details and data files)
- Version 1.0: 2016-04-13
Type: Initial release - Version 1.1: 2018-11-21
Changes: Advisory, Data collection, Derived calculations - Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description
