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- PDB-4xyw: Glycosyltransferases WbnH -

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Basic information

Entry
Database: PDB / ID: 4xyw
TitleGlycosyltransferases WbnH
ComponentsO-antigen biosynthesis glycosyltransferase WbnH
KeywordsTRANSFERASE / Glycosyltransferases WbnH GT4
Function / homologyUDP-GalNAc:alpha-D-GalNAc-diphosphoundecaprenol alpha-1,3-N-acetylgalactosaminyltransferase / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / O antigen biosynthetic process / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / hexosyltransferase activity / O-antigen biosynthesis glycosyltransferase WbnH
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsLi, F.
CitationJournal: To Be Published
Title: Glycosyltransferases WbnH
Authors: Li, F.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-antigen biosynthesis glycosyltransferase WbnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4123
Polymers38,2201
Non-polymers1922
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-17 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.311, 114.311, 183.479
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

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Components

#1: Protein O-antigen biosynthesis glycosyltransferase WbnH / UDP-GalNAc:alpha-D-GalNAc-diphosphoundecaprenol alpha-1 / 3-N-acetylgalactosaminyltransferase


Mass: 38219.988 Da / Num. of mol.: 1 / Mutation: S144N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wbnH, wbwH, wcmA / Production host: Escherichia coli (E. coli)
References: UniProt: P0DMP6, UDP-GalNAc:alpha-D-GalNAc-diphosphoundecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2M Li2SO4, 0.1M CAPS, 1.2M Sodium phosphate monobasic, 0.8M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23421 / % possible obs: 99 % / Redundancy: 11.1 % / Net I/σ(I): 23.52

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.2→26.963 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1202 5.13 %
Rwork0.2048 --
obs0.2065 23416 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→26.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 10 60 2587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0372587
X-RAY DIFFRACTIONf_angle_d2.7123500
X-RAY DIFFRACTIONf_dihedral_angle_d14.825918
X-RAY DIFFRACTIONf_chiral_restr0.377403
X-RAY DIFFRACTIONf_plane_restr0.007438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.28820.28861250.24252419X-RAY DIFFRACTION99
2.2882-2.39230.24741370.22982469X-RAY DIFFRACTION100
2.3923-2.51840.27541580.24342432X-RAY DIFFRACTION100
2.5184-2.6760.30451330.24172485X-RAY DIFFRACTION100
2.676-2.88240.25071200.23452493X-RAY DIFFRACTION100
2.8824-3.17210.27591580.22922464X-RAY DIFFRACTION100
3.1721-3.63010.26121310.21132493X-RAY DIFFRACTION100
3.6301-4.570.22021350.17232493X-RAY DIFFRACTION99
4.57-26.96520.18931050.19232466X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 24.6946 Å / Origin y: 21.5194 Å / Origin z: 78.3253 Å
111213212223313233
T0.4448 Å20.0124 Å20.0547 Å2-0.3446 Å2-0.02 Å2--0.3559 Å2
L4.4906 °21.6934 °20.275 °2-1.461 °2-0.2419 °2--0.6486 °2
S-0.0754 Å °0.0969 Å °0.1408 Å °-0.073 Å °0.0676 Å °-0.0056 Å °-0.0223 Å °-0.0586 Å °-0.0024 Å °
Refinement TLS groupSelection details: all

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