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- PDB-6pnt: Structural Characterization of UDP-glycosyltransferase from Tetra... -

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Basic information

Entry
Database: PDB / ID: 6pnt
TitleStructural Characterization of UDP-glycosyltransferase from Tetranychus Urticae
ComponentsUDP-glycosyltransferase 202A2
KeywordsTRANSFERASE / Uridine diphosphate / UDP-glycosyltransferase / Two-spotted Spider Mite / Pesticide detoxification
Function / homology: / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / nucleotide binding / membrane / UDP-glycosyltransferase 202A2
Function and homology information
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDaneshian, L. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
CitationJournal: To Be Published
Title: Structural Characterization of UDP-glycosyltransferase from Tetranychus Urticae
Authors: Daneshian, L. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
History
DepositionJul 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: UDP-glycosyltransferase 202A2


Theoretical massNumber of molelcules
Total (without water)48,9511
Polymers48,9511
Non-polymers00
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.481, 77.481, 130.953
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein UDP-glycosyltransferase 202A2


Mass: 48950.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Gene: 107367435, UGT202A2 / Plasmid: pET100/D-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: T1KUK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 10% PEG 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 39554 / % possible obs: 99.3 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.032 / Rrim(I) all: 0.09 / Rsym value: 0.083 / Net I/σ(I): 33.32
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1947 / CC1/2: 0.731 / Rpim(I) all: 0.267 / Rrim(I) all: 0.684 / Rsym value: 0.627 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IYA

2iya


Resolution: 1.85→29.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1944 4.9 %RANDOM
Rwork0.1682 ---
obs0.1701 37336 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.23 Å2 / Biso mean: 31.231 Å2 / Biso min: 19.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.22 Å2-0 Å2
2---0.45 Å20 Å2
3---1.45 Å2
Refinement stepCycle: final / Resolution: 1.85→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 0 380 3737
Biso mean---41.22 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133436
X-RAY DIFFRACTIONr_bond_other_d0.0340.0173290
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.6364651
X-RAY DIFFRACTIONr_angle_other_deg2.3161.5737660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55323.038158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0215614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8091515
X-RAY DIFFRACTIONr_chiral_restr0.1420.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023778
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02675
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 154 -
Rwork0.246 2725 -
all-2879 -
obs--99.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6058-0.1116-0.21382.3438-0.63921.66820.08990.1205-0.0429-0.3809-0.08330.01490.0777-0.0848-0.00650.1967-0.0050.01180.1169-0.00240.0034-5.3132.868-10.086
20.5881-0.4287-0.191.47210.24010.2963-0.0247-0.0730.01370.0834-0.0021-0.0544-0.00320.02390.02670.1442-0.0271-0.00160.1226-0.00210.0076-9.62944.3424.116
31.27610.61280.30260.53430.26971.1149-0.0809-0.00930.0586-0.173-0.0080.1644-0.1038-0.07590.0890.1853-0.0086-0.08220.0931-0.01050.0808-29.96350.137-10.654
45.9786-4.32420.76096.0954-1.00990.24730.12510.1950.3463-0.6566-0.2142-0.5588-0.02690.07980.08910.332-0.0260.06980.14860.01460.0523-4.27854.925-13.258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 72
2X-RAY DIFFRACTION2A73 - 259
3X-RAY DIFFRACTION3A260 - 400
4X-RAY DIFFRACTION4A401 - 436

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