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- PDB-2wzg: Legionella glucosyltransferase (Lgt1) crystal structure -

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Basic information

Entry
Database: PDB / ID: 2wzg
TitleLegionella glucosyltransferase (Lgt1) crystal structure
ComponentsGLUCOSYLTRANSFERASE
KeywordsTRANSFERASE / ELONGATION FACTOR 1A / VIRULENCE FACTOR / GLUCOSYLTRANSFERASE
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #130 / Glycosyltransferase family 88, C-terminal domain / Glycosyltransferase family 88 / Glycosyltransferase family 88 / Rna Polymerase Sigma Factor; Chain: A / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucosyltransferase Lgt1
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHurtado-Guerrero, R. / Zusman, T. / Pathak, S. / Ibrahim, A.F.M. / Shepherd, S. / Prescott, A. / Segal, G. / Van Aalten, D.M.F.
CitationJournal: Biochem.J. / Year: 2010
Title: Molecular Mechanism of Elongation Factor 1A Inhibition by a Legionella Pneumophila Glycosyltransferase.
Authors: Hurtado-Guerrero, R. / Zusman, T. / Pathak, S. / Ibrahim, A.F.M. / Shepherd, S. / Prescott, A. / Segal, G. / Van Aalten, D.M.F.
History
DepositionNov 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: audit_author / diffrn_source / entity_src_gen
Item: _audit_author.name / _diffrn_source.pdbx_synchrotron_beamline ..._audit_author.name / _diffrn_source.pdbx_synchrotron_beamline / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1243
Polymers59,5341
Non-polymers5912
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.750, 122.750, 103.416
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein GLUCOSYLTRANSFERASE /


Mass: 59533.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Plasmid: PGEX6P1 / Production host: Escherichia coli BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q5WWY0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.73 % / Description: HG WAS USED
Crystal growDetails: CRYSTALS WERE GROWN IN 0.1 M MGCL2, 12% PEG 6000, 0.1 M ACETAMIDO IMINODIACETIC ACID, PH 6.5. 2-METHYL-2,4-PENTANEDIOL (MPD) AT 20% IN MOTHER LIQUOR WAS USED AS A CRYOPROTECTANT.

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Type: ESRF / Wavelength: 1.282
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 45918 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29
Reflection shellHighest resolution: 1.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.8 / % possible all: 1

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.995 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26175 680 1.5 %RANDOM
Rwork0.19995 ---
obs0.20081 44388 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å
Displacement parametersBiso mean: 35.734 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å2-0.8 Å20 Å2
2---1.6 Å20 Å2
3---2.41 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 37 318 4365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9765810
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8775540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72824.657204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94915762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2791523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213246
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.52571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35824187
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11531696
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4884.51602
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 45 -
Rwork0.388 3078 -
obs--92.92 %

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