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- PDB-7xgx: Glucosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7xgx
TitleGlucosyltransferase
ComponentsLgt2
KeywordsTRANSFERASE / Glucosyltransferase / complex / bacterial effector
Function / homologyGlycosyltransferase family 88 / Glycosyltransferase family 88 / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucosyltransferase Lgt2
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsChen, T.T. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Small Struct / Year: 2023
Title: Structural Basis for the Action Mechanism of Legionella Glycosyltransferase.
Authors: Chen, T.T. / Zheng, S.R. / Tian, L. / Lv, S.L. / Zhong, W.H. / Li, X.L. / Zhang, D.D. / Zheng, X.X. / Ouyang, S.Y.
History
DepositionApr 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 13, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lgt2
B: Lgt2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,7954
Polymers147,6632
Non-polymers1,1332
Water2,162120
1
A: Lgt2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3982
Polymers73,8311
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-6 kcal/mol
Surface area29800 Å2
MethodPISA
2
B: Lgt2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3982
Polymers73,8311
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-6 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.055, 75.863, 126.644
Angle α, β, γ (deg.)90.000, 90.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lgt2


Mass: 73831.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: C3927_14430 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F0H5
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Calcium acetate hydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Dec 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→32.22 Å / Num. obs: 55366 / % possible obs: 95.28 % / Redundancy: 2 % / Biso Wilson estimate: 50.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02562 / Rpim(I) all: 0.02562 / Rrim(I) all: 0.03624 / Net I/σ(I): 14.72
Reflection shellResolution: 2.39→2.475 Å / Rmerge(I) obs: 0.3477 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 5597 / CC1/2: 0.867 / Rpim(I) all: 0.3477 / Rrim(I) all: 0.4917

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XGV

7xgv


Resolution: 2.39→32.22 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 1935 3.57 %
Rwork0.2154 52329 -
obs0.2172 54264 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.13 Å2 / Biso mean: 65.5673 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.39→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9475 0 116 120 9711
Biso mean--62.02 52.88 -
Num. residues----1198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.440.38721320.32423569370192
2.44-2.510.4191400.30953615375593
2.51-2.580.38211360.29993680381694
2.58-2.670.3771360.2873728386495
2.67-2.760.29721380.26513698383696
2.76-2.870.31911450.25423801394698
2.87-30.30321440.24383860400498
3-3.160.3151420.25823853399599
3.16-3.360.34211400.24693874401499
3.36-3.620.30871450.231139264071100
3.62-3.980.24631140.19982952306675
3.98-4.560.2151460.174439034049100
4.56-5.740.20521430.187839534096100
5.74-32.220.2041340.17813917405197

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