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- PDB-4rel: Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltrans... -

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Basic information

Entry
Database: PDB / ID: 4rel
TitleCrystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with kaempferol
ComponentsUDP-glucose:anthocyanidin 3-O-glucosyltransferase
KeywordsTRANSFERASE / UGT78K6 / GT-B fold / Glucosyltransferase / Complexed with kaempferol
Function / homology
Function and homology information


UDP-glycosyltransferase 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
ACETATE ION / Chem-KMP / Glycosyltransferase
Similarity search - Component
Biological speciesClitoria ternatea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.754 Å
AuthorsHiromoto, T. / Honjo, E. / Tamada, T. / Kuroki, R.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural basis for acceptor-substrate recognition of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea
Authors: Hiromoto, T. / Honjo, E. / Noda, N. / Tamada, T. / Kazuma, K. / Suzuki, M. / Blaber, M. / Kuroki, R.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose:anthocyanidin 3-O-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4587
Polymers48,7771
Non-polymers6816
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.042, 55.137, 85.880
Angle α, β, γ (deg.)90.00, 104.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-glucose:anthocyanidin 3-O-glucosyltransferase


Mass: 48777.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clitoria ternatea (plant) / Gene: Ct3GT-A / Plasmid: pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: A4F1R4, anthocyanidin 3-O-glucosyltransferase
#2: Chemical ChemComp-KMP / 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE / KAEMPHEROL


Mass: 286.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.35 Å3/Da / Density % sol: 47.59 % / Mosaicity: 0.452 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 26%(w/v) PEG 4000, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2008
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 45291 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.68 Å2 / Rmerge(I) obs: 0.06 / Χ2: 0.84 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.8130.36743930.50497.8
1.81-1.893.50.29345110.5100
1.89-1.973.70.21645030.542100
1.97-2.073.80.14745550.561100
2.07-2.23.80.10345020.618100
2.2-2.383.80.08145570.676100
2.38-2.613.80.06545250.778100
2.61-2.993.80.05245390.922100
2.99-3.773.80.04245701.32999.9
3.77-1003.70.03846361.83899.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3WC4

3wc4


Resolution: 1.754→26.163 Å / FOM work R set: 0.882 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 2284 5.05 %RANDAM
Rwork0.1594 ---
obs0.1612 45271 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.12 Å2 / Biso mean: 19.46 Å2 / Biso min: 4.58 Å2
Refinement stepCycle: LAST / Resolution: 1.754→26.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 47 408 3892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063644
X-RAY DIFFRACTIONf_angle_d1.0854974
X-RAY DIFFRACTIONf_chiral_restr0.073578
X-RAY DIFFRACTIONf_plane_restr0.005636
X-RAY DIFFRACTIONf_dihedral_angle_d13.0581339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7536-1.79170.2631140.2072536265093
1.7917-1.83340.25551520.191526262778100
1.8334-1.87930.22811340.18626912825100
1.8793-1.930.21261370.177526972834100
1.93-1.98680.22961300.170126962826100
1.9868-2.05090.23351410.162827002841100
2.0509-2.12420.20431510.153726792830100
2.1242-2.20920.18421350.149526852820100
2.2092-2.30970.17561570.153926842841100
2.3097-2.43140.19141420.1626952837100
2.4314-2.58360.24271520.168926912843100
2.5836-2.78290.21261470.166826982845100
2.7829-3.06250.20981490.17126952844100
3.0625-3.50480.18961410.161927112852100
3.5048-4.41220.17551430.138327332876100
4.4122-26.16550.15141590.14752770292999
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)
10.3778-0.08310.23420.5864-0.23140.48620.0161-0.003-0.0031-0.019-0.01860.00820.01390.006-0.02530.0233-0.00130.01240.0394-0.00970.020155.9555.957115.9002
20.7380.7016-0.03120.57790.14780.1902-0.02010.00820.02250.04410.04420.04280.00270.01170.01680.07250.0151-0.00290.07330.00450.087144.0639-8.120632.1487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 1 through 248 )A1 - 248
2X-RAY DIFFRACTION2chain A and (resid 249 through 446 )A249 - 446

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