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- PDB-8j2z: Glucosyl transferase -

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Basic information

Entry
Database: PDB / ID: 8j2z
TitleGlucosyl transferase
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glucosyl transferase
Function / homologyUDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / Glycosyltransferase
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.783 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technology Saudi Arabia
CitationJournal: To Be Published
Title: Glucosyl transferase
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionApr 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)53,9461
Polymers53,9461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.384, 153.384, 126.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Glycosyltransferase


Mass: 53945.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8K1ZRH3

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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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES pH 7.5, 30% v/vPEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.783→48.5 Å / Num. obs: 19066 / % possible obs: 98.23 % / Redundancy: 25.9 % / CC1/2: 0.991 / Net I/σ(I): 7.64
Reflection shellResolution: 2.783→2.883 Å / Num. unique obs: 1570 / CC1/2: 0.445

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.783→48.5 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2768 1892 10 %
Rwork0.2231 --
obs0.2286 18916 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.783→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 0 0 3572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.172
X-RAY DIFFRACTIONf_dihedral_angle_d6.828480
X-RAY DIFFRACTIONf_chiral_restr0.061584
X-RAY DIFFRACTIONf_plane_restr0.01624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.783-2.850.41641030.3756922X-RAY DIFFRACTION76
2.85-2.930.39221350.31341217X-RAY DIFFRACTION100
2.93-3.020.36021350.29681216X-RAY DIFFRACTION100
3.02-3.110.35311330.2861206X-RAY DIFFRACTION100
3.11-3.220.3031370.28641224X-RAY DIFFRACTION100
3.22-3.350.35611360.27651222X-RAY DIFFRACTION100
3.35-3.510.35141350.25181224X-RAY DIFFRACTION100
3.51-3.690.30841380.23941233X-RAY DIFFRACTION100
3.69-3.920.25671360.23111227X-RAY DIFFRACTION100
3.92-4.230.28371380.20491234X-RAY DIFFRACTION100
4.23-4.650.25031380.19291242X-RAY DIFFRACTION100
4.65-5.320.24721380.18461250X-RAY DIFFRACTION100
5.32-6.70.27581400.24831265X-RAY DIFFRACTION100
6.7-48.50.21311500.17451342X-RAY DIFFRACTION100

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