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

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Basic information

Entry
Database: PDB / ID: 4rem
TitleCrystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with delphinidin
ComponentsUDP-glucose:anthocyanidin 3-O-glucosyltransferase
KeywordsTRANSFERASE / UGT78K6 / GT-B fold / Glucosyltransferase / Complexed with delphinidin
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
Chem-DLM / Glycosyltransferase
Similarity search - Component
Biological speciesClitoria ternatea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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)49,3575
Polymers48,7771
Non-polymers5804
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.021, 55.121, 85.958
Angle α, β, γ (deg.)90.00, 104.57, 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-DLM / 3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)chromenium / Delphinidin


Mass: 303.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11O7
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 47.69 % / Mosaicity: 0.694 °
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: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 12, 2008
RadiationMonochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 14870 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.14 Å2 / Rmerge(I) obs: 0.099 / Χ2: 2.522 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.55-2.643.70.32314822.37199.9
2.64-2.753.70.28314942.27599.9
2.75-2.873.70.23614582.39399.9
2.87-3.023.70.19414672.33199.8
3.02-3.213.70.15714832.4399.7
3.21-3.463.60.11314862.63799.3
3.46-3.813.60.08314852.5699.7
3.81-4.363.60.06514782.77899.1
4.36-5.493.60.05915032.7998.8
5.49-503.50.05115342.66399.2

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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: 2.55→37.905 Å / FOM work R set: 0.8437 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 750 5.05 %RANDOM
Rwork0.1811 ---
obs0.1838 14854 99.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.73 Å2 / Biso mean: 32.43 Å2 / Biso min: 5.27 Å2
Refinement stepCycle: LAST / Resolution: 2.55→37.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 40 127 3604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033583
X-RAY DIFFRACTIONf_angle_d0.7484883
X-RAY DIFFRACTIONf_chiral_restr0.05570
X-RAY DIFFRACTIONf_plane_restr0.003622
X-RAY DIFFRACTIONf_dihedral_angle_d13.3041302
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5496-2.74640.31081450.2262766291198
2.7464-3.02270.31151500.217228042954100
3.0227-3.45980.24711600.20292820298099
3.4598-4.3580.21371390.15672824296399
4.358-37.90880.1821560.15742890304699
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)
10.2650.15640.10970.6106-0.13140.7117-0.01460.0211-0.00670.0172-0.00080.0147-0.0060.0060.00070.03130.00350.00630.059-0.01290.05136.05856.417715.9329
20.60680.35150.01830.3062-0.02360.2441-0.0220.02030.02020.01710.0780.08380.00430.010400.13530.01040.00110.1243-0.00170.1458-5.7016-7.604132.1823
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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