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- PDB-8xfh: Crystal structure of MiCGT(E152Q/V190D/S122P) in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 8xfh
TitleCrystal structure of MiCGT(E152Q/V190D/S122P) 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: 2.80000300155 Å
AuthorsZhang, Z.M. / Zhou, Z.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of MiCGT(E152Q/V190D/S122P) in complex with UDP
Authors: Zhang, Z.M. / Zhou, Z.Q.
History
DepositionDec 13, 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)103,6404
Polymers102,8322
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-9 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.532, 103.354, 108.966
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


Mass: 51415.922 Da / Num. of mol.: 2 / Mutation: S122P, E152Q, V190D
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
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / 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: 2.8→47.15 Å / Num. obs: 26288 / % possible obs: 99.32 % / Redundancy: 12.8 % / Biso Wilson estimate: 58.6869915508 Å2 / CC1/2: 0.969 / Net I/σ(I): 2.1
Reflection shellResolution: 2.902→3.005 Å / Num. unique obs: 6917 / CC1/2: 0.969

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.80000300155→37.4939106389 Å / SU ML: 0.358095563705 / Cross valid method: FREE R-VALUE / σ(F): 1.35397126728 / Phase error: 25.4054548227
RfactorNum. reflection% reflection
Rfree0.244109439651 1979 7.52814972611 %
Rwork0.221176572174 24309 -
obs0.222902956102 26288 99.7344259807 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.0269374521 Å2
Refinement stepCycle: LAST / Resolution: 2.80000300155→37.4939106389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6644 0 50 0 6694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003202067430266868
X-RAY DIFFRACTIONf_angle_d0.8342708289619397
X-RAY DIFFRACTIONf_chiral_restr0.02758198866011082
X-RAY DIFFRACTIONf_plane_restr0.004268754905181206
X-RAY DIFFRACTIONf_dihedral_angle_d15.79373716042387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.870.3188456101291360.3000349966041699X-RAY DIFFRACTION99.9455337691
2.87-2.94760.3264801840081330.2860914529831725X-RAY DIFFRACTION99.8387963461
2.9476-3.03430.3355326345531470.2859669911071690X-RAY DIFFRACTION99.8369565217
3.0343-3.13220.2986740314151350.2781324174011713X-RAY DIFFRACTION99.9459167117
3.1322-3.2440.2997909720661440.2807149478981716X-RAY DIFFRACTION100
3.244-3.37380.2716224759641300.2466585708881709X-RAY DIFFRACTION99.8913633895
3.3738-3.52730.2591687589331370.2419235426031750X-RAY DIFFRACTION99.9470338983
3.5273-3.71310.2594889864741430.233146937521728X-RAY DIFFRACTION100
3.7131-3.94550.2338189573951410.2093958299651724X-RAY DIFFRACTION99.9464094319
3.9455-4.24980.2369934478971450.1940947633551742X-RAY DIFFRACTION99.9470338983
4.2498-4.67670.1888518836671470.1928929631671743X-RAY DIFFRACTION99.8942917548
4.6767-5.35180.2193558269371410.2015150322671761X-RAY DIFFRACTION99.8949579832
5.3518-6.73630.2441918660851430.216968613751779X-RAY DIFFRACTION99.896049896
6.7363-37.490.2131519546811570.1902705752331830X-RAY DIFFRACTION97.5454099165

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