7O2N | pdb_00007o2n

Crystal structure of B. subtilis UGPase YngB

PDB DOI: https://doi.org/10.2210/pdb7O2N/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-30 Released: 2021-04-14
Deposition Author(s): Wu, C.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.264 (Depositor), 0.266 (DCC)
R-Value Work:
0.213 (Depositor), 0.215 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7O2N

This is version 1.2 of the entry. See complete history.

Literature

Structural and Functional Characterisation of the Bacillus subtilis Uridylyltransferase YngB

(2021) Ph D Thesis

DOI: https://doi.org/10.25560/91986

Macromolecule Content

Total Structure Weight: 66.12 kDa
Atom Count: 4,383
Modeled Residue Count: 580
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable UTP--glucose-1-phosphate uridylyltransferase YngB	A, B	296	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: yngB, BSU18180 EC: 2.7.7.9
UniProt
Find proteins for O31822 (Bacillus subtilis (strain 168)) Explore O31822 Go to UniProtKB: O31822
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31822
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.264 (Depositor), 0.266 (DCC)
R-Value Work: 0.213 (Depositor), 0.215 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.156	α = 90
b = 158.979	β = 90
c = 180.317	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2021-04-14
Type: Initial release
Version 1.1: 2021-10-27
Changes: Data collection, Database references
Version 1.2: 2024-01-31
Changes: Data collection, Database references, Refinement description

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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.