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- PDB-4wad: Crystal Structure of TarM with UDP-GlcNAc -

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Basic information

Entry
Database: PDB / ID: 4wad
TitleCrystal Structure of TarM with UDP-GlcNAc
ComponentsGlycosyl transferase, group 1 family proteinGlycosyltransferase
KeywordsTRANSFERASE / GT-B fold / GT-4 / retaining glycosyltransferase / DUF1975 / Rossmann fold / WTA-binding
Function / homology
Function and homology information


poly(glycerol-phosphate) alpha-glucosyltransferase / poly(glycerol-phosphate) alpha-glucosyltransferase activity / dextransucrase activity / dextransucrase
Similarity search - Function
Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Glycosyl transferase family 1 / Glycosyl transferase, group 1 family protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKoc, C. / Stehle, T. / Xia, G. / Peschel, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Enzymatic Analysis of TarM Glycosyltransferase from Staphylococcus aureus Reveals an Oligomeric Protein Specific for the Glycosylation of Wall Teichoic Acid.
Authors: Koc, C. / Gerlach, D. / Beck, S. / Peschel, A. / Xia, G. / Stehle, T.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / software / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl transferase, group 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7406
Polymers57,9371
Non-polymers8025
Water81145
1
A: Glycosyl transferase, group 1 family protein
hetero molecules

A: Glycosyl transferase, group 1 family protein
hetero molecules

A: Glycosyl transferase, group 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,21918
Polymers173,8123
Non-polymers2,40715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area9240 Å2
ΔGint-75 kcal/mol
Surface area67690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.024, 124.024, 217.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

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Components

#1: Protein Glycosyl transferase, group 1 family protein / Glycosyltransferase / TarM


Mass: 57937.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pBAD-TOPO-102 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q2FI41, UniProt: A0A0D6HUA0*PLUS, dextransucrase, poly(glycerol-phosphate) alpha-glucosyltransferase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.16 Å3/Da / Density % sol: 70.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Magnesium-chloride, PEG-8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24904 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 57.67 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.234 / Rrim(I) all: 0.243 / Χ2: 0.967 / Net I/σ(I): 11.69 / Num. measured all: 326267
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.870.4792.2631.2724252182218222.355100
2.87-2.950.5331.6661.7724688180318021.73399.9
2.95-3.040.671.3792.123415172317231.435100
3.04-3.130.7281.0852.6622582167416731.12999.9
3.13-3.230.860.783.6521789162916280.81299.9
3.23-3.350.9260.5665.0421159159815970.58999.9
3.35-3.470.9450.4436.2619705152515240.46299.9
3.47-3.610.9690.3048.4618407147614750.31799.9
3.61-3.780.9740.24610.1316572142514220.25899.8
3.78-3.960.9880.22111.5916680136113380.2398.3
3.96-4.170.9950.1715.2517398131113080.17799.8
4.17-4.430.9950.12819.916773123512300.13399.6
4.43-4.730.9970.10223.815493116711620.10599.6
4.73-5.110.9970.10922.0214356109510900.11499.5
5.11-5.60.9960.12719.8113092101710110.13299.4
5.6-6.260.9960.12519.75116639369300.1399.4
6.26-7.230.9960.11320.490648238170.11899.3
7.23-8.850.9990.06631.8384627217040.06997.6
8.85-12.5210.04445.3372105815700.04598.1
12.5210.03745.2435073623400.03993.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.45
Highest resolutionLowest resolution
Rotation48.13 Å3.5 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WAC

4wac


Resolution: 2.8→48.132 Å / FOM work R set: 0.7521 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2939 1246 5 %
Rwork0.2518 23652 -
obs0.2539 24898 99.4 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.3 Å2 / Biso mean: 70.58 Å2 / Biso min: 24.29 Å2
Refinement stepCycle: final / Resolution: 2.8→48.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 49 45 4168
Biso mean--84.51 46.47 -
Num. residues----498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044200
X-RAY DIFFRACTIONf_angle_d0.7995642
X-RAY DIFFRACTIONf_chiral_restr0.032614
X-RAY DIFFRACTIONf_plane_restr0.003715
X-RAY DIFFRACTIONf_dihedral_angle_d14.1951605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8003-2.91240.37831340.2992537267198
2.9124-3.04490.35571360.29225832719100
3.0449-3.20540.33361360.273225922728100
3.2054-3.40620.2891360.251325802716100
3.4062-3.66910.26361380.233326192757100
3.6691-4.03820.25671370.23392596273399
4.0382-4.62210.23651390.222726452784100
4.6221-5.82180.2851410.257926712812100
5.8218-48.13920.35241490.26552829297898

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