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- PDB-2acv: Crystal Structure of Medicago truncatula UGT71G1 -

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Basic information

Entry
Database: PDB / ID: 2acv
TitleCrystal Structure of Medicago truncatula UGT71G1
Componentstriterpene UDP-glucosyl transferase UGT71G1
KeywordsTRANSFERASE / Glycosyltransferase / UDP
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsShao, H. / He, X. / Achnine, L. / Blount, J.W. / Dixon, R.A. / Wang, X.
CitationJournal: Plant Cell / Year: 2005
Title: Crystal Structures of a Multifunctional Triterpene/Flavonoid Glycosyltransferase from Medicago truncatula.
Authors: Shao, H. / He, X. / Achnine, L. / Blount, J.W. / Dixon, R.A. / Wang, X.
History
DepositionJul 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: triterpene UDP-glucosyl transferase UGT71G1
B: triterpene UDP-glucosyl transferase UGT71G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0794
Polymers103,2712
Non-polymers8082
Water13,115728
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.713, 90.593, 101.788
Angle α, β, γ (deg.)90, 102.567, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein triterpene UDP-glucosyl transferase UGT71G1


Mass: 51635.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: UGT71G1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5IFH7, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.6 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 3350, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.5418
SYNCHROTRONCAMD GCPCC20.9797, 0.97996, 0.9393
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEJan 3, 2005
MARRESEARCH2CCDFeb 9, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Osmic Confocal Max-FluxSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97971
30.979961
40.93931
ReflectionResolution: 2→100 Å / Num. all: 62825 / Num. obs: 62825 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 2.7 / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→66.94 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4980 -RANDOM
Rwork0.187 ---
all0.206 60990 --
obs0.206 60990 94.8 %-
Displacement parametersBiso mean: 31.841 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2→66.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7204 0 50 728 7982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.27

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