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- PDB-3wc4: Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltrans... -

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Basic information

Entry
Database: PDB / ID: 3wc4
TitleCrystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea
ComponentsUDP-glucose:anthocyanidin 3-O-glucosyltransferase
KeywordsTRANSFERASE / GT-B fold / Glucosyltransferase / UDP-glucose/Anthocyanidin binding / Glucosylation
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 / Glycosyltransferase
Similarity search - Component
Biological speciesClitoria ternatea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsHiromoto, T. / Honjo, E. / Tamada, T. / Kuroki, R.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2013
Title: Crystal structure of UDP-glucose:anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea
Authors: Hiromoto, T. / Honjo, E. / Tamada, T. / Noda, N. / Kazuma, K. / Suzuki, M. / Kuroki, R.
History
DepositionMay 24, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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)49,0204
Polymers48,7771
Non-polymers2433
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.202, 55.195, 86.224
Angle α, β, γ (deg.)90.00, 105.07, 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: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: A4F1R4, anthocyanidin 3-O-glucosyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.36 Å3/Da / Density % sol: 47.99 % / Mosaicity: 0.888 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate tribasic, 0.2M ammonium acetate, 26%(w/v) PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 27, 2008
RadiationMonochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 38850 / Num. obs: 38766 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.099 / Χ2: 2.908 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.60.42238562.044199.2
1.92-1.993.70.31138372.094199.4
1.99-2.083.70.22938912.297199.5
2.08-2.193.70.18138832.541199.6
2.19-2.333.70.15938522.847199.5
2.33-2.513.60.13838703.129199.2
2.51-2.763.60.11538863.376199.4
2.76-3.163.50.09138753.588199.2
3.16-3.993.50.06338543.763198.1
3.99-503.40.05239623.555198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C1Z

2c1z


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2048 / WRfactor Rwork: 0.1633 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8677 / SU B: 5.323 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1391 / SU Rfree: 0.1301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1935 5 %RANDOM
Rwork0.17 ---
obs0.172 38744 98.89 %-
all-39179 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.61 Å2 / Biso mean: 19.9 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.2 Å2
2---0.85 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 16 436 3888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023589
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9714899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59224.718142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31315604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8951514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212679
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 122 -
Rwork0.235 2554 -
all-2676 -
obs--96.36 %
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)
10.9391-0.23860.39641.3398-0.44651.06180.0077-0.0408-0.05760.0235-0.01020.04580.0259-0.01840.00250.0057-0.00790.00570.0139-0.00560.01045.7016.21215.972
21.86161.5107-0.31191.7633-0.2510.50270.00060.06520.05030.01410.04930.0906-0.0031-0.0534-0.04990.04590.0387-0.00990.0534-0.00550.0312-6.332-7.88432.226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 248
2X-RAY DIFFRACTION2A249 - 446

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