Download MendeleyCrystal structure of the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
Muzzolini, L., Versees, W., Steyaert, J., Degano, M.To be published.
1YOE
Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
- PDB DOI: https://doi.org/10.2210/pdb1YOE/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2005-01-27 Released: 2006-01-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.78 ?
- R-Value Free: 0.193
- R-Value Work: 0.167
- R-Value Observed: 0.168
Starting Model: experimental
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This is version 2.1 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 |
| Hypothetical protein ybeK | 322 | Escherichia coli | Mutation(s): 0 Gene Names: ybeK/rihA EC: 3.2.2.8 (PDB Primary Data), 3.2 (UniProt) |  | |
UniProt | |||||
Find proteins for P41409 (Escherichia coli (strain K12)) Explore P41409 Go to UniProtKB: P41409 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P41409 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| RIB Query on RIB | B [auth A] | alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N |  | ||
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.78 ?
- R-Value Free: 0.193
- R-Value Work: 0.167
- R-Value Observed: 0.168
- Space Group: I 2 2 2
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 76.466 | ¦Á = 90 |
| b = 84.062 | ¦Â = 90 |
| c = 112.483 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2006-01-17 Deposition Author(s): Muzzolini, L., Versees, W., Steyaert, J., Degano, M.
Revision History (Full details and data files)
- Version 1.0: 2006-01-17
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
