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- PDB-8xfw: Crystal structure of MiCGT(M148A/V190T/S121D) in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 8xfw
TitleCrystal structure of MiCGT(M148A/V190T/S121D) in complex with UDP
ComponentsUDP-glycosyltransferase 13
KeywordsTRANSFERASE
Function / homology
Function and homology information


xylosyltransferase activity / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
: / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 13
Similarity search - Component
Biological speciesMangifera indica (mango)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1000561844 Å
AuthorsZhang, Z.M. / Zhou, Z.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of MiCGT(M148A/V190T/S121D) in complex with UDP
Authors: Zhang, Z.M. / Zhou, Z.Q.
History
DepositionDec 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 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: UDP-glycosyltransferase 13
B: UDP-glycosyltransferase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3133
Polymers101,9092
Non-polymers4041
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-10 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.194, 103.617, 110.195
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein UDP-glycosyltransferase 13 / MiUGT13 / C-glycosyltransferase / MiCGT


Mass: 50954.281 Da / Num. of mol.: 2 / Mutation: S121P, M148A, V190T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mangifera indica (mango) / Gene: CGT / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0M4KE44, Transferases; Glycosyltransferases; Hexosyltransferases
#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
Has ligand of interestY
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 277 K / Method: evaporation, recrystallization / pH: 7
Details: 200mM calcium acetate,100mM tris (PH 6.5-7.5),PEG 3000 16%-22%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.1→29.97 Å / Num. obs: 37033 / % possible obs: 99.82 % / Redundancy: 10.9 % / Biso Wilson estimate: 55.5650163647 Å2 / CC1/2: 0.98 / Net I/σ(I): 9.17
Reflection shellResolution: 3.1→3.211 Å / Num. unique obs: 6919 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data reduction
PHASESphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1000561844→29.97 Å / SU ML: 0.417611062628 / Cross valid method: FREE R-VALUE / σ(F): 1.34757244333 / Phase error: 23.364801161
RfactorNum. reflection% reflection
Rfree0.239484511891 2585 6.98026084843 %
Rwork0.191873487858 34448 -
obs0.195197003472 37033 99.0054805507 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.4026683338 Å2
Refinement stepCycle: LAST / Resolution: 3.1000561844→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 25 0 6683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003607969469846854
X-RAY DIFFRACTIONf_angle_d0.8177588562639371
X-RAY DIFFRACTIONf_chiral_restr0.02947735856491082
X-RAY DIFFRACTIONf_plane_restr0.003862387443361205
X-RAY DIFFRACTIONf_dihedral_angle_d15.20854581512381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.15970.4554098891631280.3311952314031736X-RAY DIFFRACTION89.1866028708
3.1597-3.22410.3083196781351320.2921323422381895X-RAY DIFFRACTION96.9392635103
3.2241-3.29420.2882389739531510.2471292409911910X-RAY DIFFRACTION100
3.2942-3.37080.2814758445381440.2326946002851898X-RAY DIFFRACTION99.70703125
3.3708-3.45510.3208424887421490.2388356048871959X-RAY DIFFRACTION99.6690307329
3.4551-3.54840.2850354847881460.2251636428051919X-RAY DIFFRACTION100
3.5484-3.65280.2552764539951340.2088483412711928X-RAY DIFFRACTION99.8063891578
3.6528-3.77060.2509602935831500.1878741129991936X-RAY DIFFRACTION99.9042145594
3.7706-3.90530.2411850217411410.1789602811411906X-RAY DIFFRACTION99.8536585366
3.9053-4.06160.1955359684631490.1768670022811955X-RAY DIFFRACTION100
4.0616-4.24630.2163934590281380.1711122502791932X-RAY DIFFRACTION99.9034749035
4.2463-4.46990.2047826225521460.1528380646221925X-RAY DIFFRACTION99.8553519769
4.4699-4.74960.2012598518731450.1517962809731927X-RAY DIFFRACTION100
4.7496-5.11580.2119896772961420.1541572955041938X-RAY DIFFRACTION99.9039385207
5.1158-5.62950.2321072564441450.1821857096441921X-RAY DIFFRACTION99.8550024166
5.6295-6.44170.2488539137151480.1984393182071937X-RAY DIFFRACTION99.7607655502
6.4417-8.10670.2481375207461530.19550187461928X-RAY DIFFRACTION99.9039846375
8-270.1881047118581440.1707164352341898X-RAY DIFFRACTION98.0787704131

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