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- PDB-7o2n: Crystal structure of B. subtilis UGPase YngB -

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Basic information

Entry
Database: PDB / ID: 7o2n
TitleCrystal structure of B. subtilis UGPase YngB
ComponentsProbable UTP--glucose-1-phosphate uridylyltransferase YngB
KeywordsTRANSFERASE / UTP / glucose-1-phosphate / UDP-glucose
Function / homologyUTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / enterobacterial common antigen biosynthetic process / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases / UTP--glucose-1-phosphate uridylyltransferase YngB
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWu, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationBook title: Ph.D.Thesis / Journal: Ph.D.Thesis / Year: 2021
Title: Structural and Functional Characterisation of the Bacillus subtilis Uridylyltransferase YngB
Authors: Wu, C.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.book_title / _citation.country ..._citation.book_title / _citation.country / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable UTP--glucose-1-phosphate uridylyltransferase YngB
B: Probable UTP--glucose-1-phosphate uridylyltransferase YngB


Theoretical massNumber of molelcules
Total (without water)66,1202
Polymers66,1202
Non-polymers00
Water86548
1
A: Probable UTP--glucose-1-phosphate uridylyltransferase YngB

B: Probable UTP--glucose-1-phosphate uridylyltransferase YngB


Theoretical massNumber of molelcules
Total (without water)66,1202
Polymers66,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area4700 Å2
ΔGint-33 kcal/mol
Surface area25820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.156, 158.979, 180.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-312-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 4 - 296 / Label seq-ID: 3 - 295

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable UTP--glucose-1-phosphate uridylyltransferase YngB / Alpha-D-glucosyl-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / Uridine ...Alpha-D-glucosyl-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / Uridine diphosphoglucose pyrophosphorylase


Mass: 33059.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yngB, BSU18180 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O31822, UTP-glucose-1-phosphate uridylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium citrate tribasic monohydrate, 0.05M lithium citrate tribasic tetrahydrate, 0.1M sodium phosphate monobasic monohydrate, 21% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→56.29 Å / Num. obs: 19691 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rrim(I) all: 0.065 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.95 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2814 / CC1/2: 0.91 / Rrim(I) all: 0.397

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B1R

7b1r


Resolution: 2.8→56.29 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 19.244 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.176 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 985 5 %RANDOM
Rwork0.213 ---
obs0.2157 18699 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.23 Å2 / Biso mean: 70.184 Å2 / Biso min: 33.55 Å2
Baniso -1Baniso -2Baniso -3
1-6.93 Å20 Å20 Å2
2---6.62 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.8→56.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4335 0 0 48 4383
Biso mean---61.15 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124400
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6345972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6535576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61322.767206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.11415738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5081527
X-RAY DIFFRACTIONr_chiral_restr0.1420.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023314
Refine LS restraints NCS

Ens-ID: 1 / Number: 8033 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 72 -
Rwork0.416 1341 -
all-1413 -
obs--99.79 %

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