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- PDB-7xgv: Legionella glucosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7xgv
TitleLegionella glucosyltransferase
ComponentsLgt2
KeywordsTRANSFERASE / Glucosyltransferase / bacterial effector
Function / homologyGlycosyltransferase family 88 / Glycosyltransferase family 88 / Glucosyltransferase Lgt2
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 6, 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


Theoretical massNumber of molelcules
Total (without water)147,5422
Polymers147,5422
Non-polymers00
Water9,728540
1
A: Lgt2


Theoretical massNumber of molelcules
Total (without water)73,7711
Polymers73,7711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lgt2


Theoretical massNumber of molelcules
Total (without water)73,7711
Polymers73,7711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.181, 76.014, 126.579
Angle α, β, γ (deg.)90.000, 90.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lgt2


Mass: 73771.242 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
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: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→29.22 Å / Num. obs: 66028 / % possible obs: 97.3 % / Redundancy: 2 % / Biso Wilson estimate: 44.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02234 / Rpim(I) all: 0.02234 / Rrim(I) all: 0.0316 / Net I/σ(I): 16.27
Reflection shellResolution: 2.27→2.351 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2474 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 64406 / CC1/2: 0.951 / Rpim(I) all: 0.2474 / Rrim(I) all: 0.3499 / % possible all: 92.6

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18_3845refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JSZ

3jsz


Resolution: 2.27→29.22 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1969 3.04 %
Rwork0.2058 62817 -
obs0.2073 64786 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.73 Å2 / Biso mean: 62.071 Å2 / Biso min: 28.55 Å2
Refinement stepCycle: final / Resolution: 2.27→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9554 0 0 540 10094
Biso mean---56.94 -
Num. residues----1209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.27-2.320.34411330.3006419892
2.32-2.380.35311320.2838430593
2.38-2.450.33261310.2587434695
2.45-2.530.34541430.2544437895
2.53-2.620.37231410.2497440496
2.62-2.730.30091320.2393444597
2.73-2.850.31661370.2358451798
2.85-30.3141440.2203456499
3-3.190.27161440.2204455599
3.19-3.440.23921480.2156459499
3.44-3.780.29041410.19864615100
3.78-4.330.22691420.17934589100
4.33-5.450.20151500.17164657100
5.45-29.220.20771510.1931465098

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