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- PDB-7lvy: Crystal Structure of Tetur04g02350 -

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Basic information

Entry
Database: PDB / ID: 7lvy
TitleCrystal Structure of Tetur04g02350
ComponentsUDP-glycosyltransferase 203A2
KeywordsTRANSFERASE
Function / homology: / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / nucleotide binding / beta-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 203A2
Function and homology information
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDanehsian, L. / Kluza, A. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2020-67014-31179 United States
CitationJournal: To Be Published
Title: Crystal Structure of Tetur04g02350
Authors: Danehsian, L. / Kluza, A. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
History
DepositionFeb 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glycosyltransferase 203A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4624
Polymers52,6971
Non-polymers7643
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.159, 61.596, 78.861
Angle α, β, γ (deg.)90.000, 106.150, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UDP-glycosyltransferase 203A2


Mass: 52697.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Gene: 107359436, UGT203A2 / Production host: Escherichia coli (E. coli) / References: UniProt: T1K1R5
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M DL-Malic acid

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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: Aug 6, 2020
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: 41813 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Rsym value: 0.058 / Net I/σ(I): 23.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2095 / CC1/2: 0.867 / CC star: 0.964 / Rpim(I) all: 0.309 / Rrim(I) all: 0.573 / Rsym value: 0.479 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PNT

6pnt


Resolution: 1.85→38.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.422 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 2001 4.8 %RANDOM
Rwork0.1818 ---
obs0.1835 39812 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.1 Å2 / Biso mean: 32.675 Å2 / Biso min: 20.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å2-1.31 Å2
2---1.18 Å20 Å2
3----1.61 Å2
Refinement stepCycle: final / Resolution: 1.85→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 49 358 3869
Biso mean--38.58 41.75 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133618
X-RAY DIFFRACTIONr_bond_other_d0.0340.0173424
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.664903
X-RAY DIFFRACTIONr_angle_other_deg2.2751.5957947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3423.352182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1615635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0071516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023989
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02783
LS refinement shellResolution: 1.854→1.902 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 151 -
Rwork0.322 2816 -
all-2967 -
obs--93.8 %
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)
12.4509-0.92950.69911.07570.01091.2976-0.04240.10540.06480.03540.0292-0.0323-0.28840.17160.01320.1776-0.01720.06220.19940.01210.043235.315.07821.511
20.36860.03430.18230.41910.12931.1711-0.0425-0.0785-0.02170.0730.05510.00550.04760.0137-0.01260.15590.01820.09140.2020.01470.059330.407-0.77530.067
30.7857-0.1693-0.00235.65131.42811.6276-0.0745-0.18120.00170.06270.08380.01830.0724-0.0285-0.00930.13220.01650.07010.20190.01410.042429.7070.31343.549
40.3908-0.1313-0.02240.6140.60211.467-0.01740.0412-0.0418-0.03140.0854-0.0180.04090.1173-0.0680.1358-0.00920.08270.2094-0.00540.062132.579-5.26210.53
50.6108-0.8543-0.82253.8473.08773.1645-0.07150.0122-0.0757-0.1279-0.05590.3023-0.2057-0.16790.12730.12560.02910.04450.20640.00950.057117.1925.77111.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 62
2X-RAY DIFFRACTION2A63 - 180
3X-RAY DIFFRACTION3A181 - 202
4X-RAY DIFFRACTION4A203 - 386
5X-RAY DIFFRACTION5A387 - 426

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