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- PDB-5n7z: glycosyltransferase in LPS biosynthesis -

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Basic information

Entry
Database: PDB / ID: 5n7z
Titleglycosyltransferase in LPS biosynthesis
ComponentsLipopolysaccharide 1,6-galactosyltransferase
KeywordsTRANSFERASE / glycosyltransferase LPS biosynthesis
Function / homologyGlycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / lipopolysaccharide core region biosynthetic process / Glycosyl transferases group 1 / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / Lipopolysaccharide 1,6-galactosyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsAshworth, G.J. / Zhang, Z.
CitationJournal: To Be Published
Title: glycosyltransferase in LPS biosynthesis
Authors: Ashworth, G.J. / Zhang, Z.
History
DepositionFeb 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipopolysaccharide 1,6-galactosyltransferase


Theoretical massNumber of molelcules
Total (without water)40,9431
Polymers40,9431
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.270, 104.270, 88.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

#1: Protein Lipopolysaccharide 1,6-galactosyltransferase / UDP-D-galactose--(Glucosyl)lipopolysaccharide-alpha-1 / 3-D-galactosyltransferase


Mass: 40943.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: rfaB, waaB, STM3719 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q06994, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 298.15 K / Method: evaporation
Details: 1% trypton; 0.001M sodium azide; 0.05M HEPES pH7.0 and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.8233 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8233 Å / Relative weight: 1
ReflectionResolution: 1.81→67.64 Å / Num. obs: 44340 / % possible obs: 98.5 % / Redundancy: 18.2 % / Net I/σ(I): 3.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data collection
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→67.446 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 2.03 / Phase error: 24.94
RfactorNum. reflection% reflection
Rfree0.2591 2225 5.03 %
Rwork0.2294 --
obs0.2309 44275 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→67.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 0 92 2929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082912
X-RAY DIFFRACTIONf_angle_d13940
X-RAY DIFFRACTIONf_dihedral_angle_d13.8131719
X-RAY DIFFRACTIONf_chiral_restr0.064425
X-RAY DIFFRACTIONf_plane_restr0.006500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.84940.35531130.30652218X-RAY DIFFRACTION84
1.8494-1.89240.31931340.27752448X-RAY DIFFRACTION94
1.8924-1.93970.28361440.25912553X-RAY DIFFRACTION97
1.9397-1.99220.29511260.24832626X-RAY DIFFRACTION100
1.9922-2.05080.28891300.24842649X-RAY DIFFRACTION100
2.0508-2.1170.26681410.25422626X-RAY DIFFRACTION100
2.117-2.19270.34091380.25582630X-RAY DIFFRACTION100
2.1927-2.28050.26271400.2482663X-RAY DIFFRACTION100
2.2805-2.38430.26091480.2542647X-RAY DIFFRACTION100
2.3843-2.510.30831360.25762637X-RAY DIFFRACTION100
2.51-2.66720.26891590.26272650X-RAY DIFFRACTION100
2.6672-2.87320.29881440.26232671X-RAY DIFFRACTION100
2.8732-3.16230.2851480.26352688X-RAY DIFFRACTION100
3.1623-3.61990.27281320.23532704X-RAY DIFFRACTION100
3.6199-4.56050.20541500.1832740X-RAY DIFFRACTION100
4.5605-67.49320.19881420.17172900X-RAY DIFFRACTION100

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