1YOE | pdb_00001yoe

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
Deposition Author(s): Muzzolini, L., Versees, W., Steyaert, J., Degano, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.193 (Depositor), 0.187 (DCC)
R-Value Work:
0.167 (Depositor), 0.163 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose

Muzzolini, L., Versees, W., Steyaert, J., Degano, M.

To be published.

Macromolecule Content

Total Structure Weight: 35.32 kDa
Atom Count: 2,565
Modeled Residue Count: 302
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ybeK	A	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41409
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIB Query on RIB Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	alpha-D-ribofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-AIHAYLRMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.193 (Depositor), 0.187 (DCC)
R-Value Work: 0.167 (Depositor), 0.163 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.466	α = 90
b = 84.062	β = 90
c = 112.483	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-01-17

Deposition Author(s):

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.