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

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Basic information

Entry
Database: PDB / ID: 4whm
TitleCrystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with UDP
ComponentsUDP-glucose:anthocyanidin 3-O-glucosyltransferase
KeywordsTRANSFERASE / Ct3GT-A / UGT78K6 / GT-B fold / Complexed with UDP
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 / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesClitoria ternatea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 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 1.1Mar 11, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)49,4255
Polymers48,7771
Non-polymers6474
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-10 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.059, 55.335, 85.517
Angle α, β, γ (deg.)90.000, 105.040, 90.000
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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 486 / 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: 47.55 %
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

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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: 1.85→50 Å / Num. obs: 38569 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.45 Å2 / Rmerge(I) obs: 0.083 / Χ2: 0.915 / Net I/av σ(I): 15.2 / Net I/σ(I): 8.8 / Num. measured all: 142408
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.85-1.923.10.3742.137500.57397.5
1.92-1.993.50.32738210.59199.6
1.99-2.083.70.24138390.635100
2.08-2.193.80.17638750.665100
2.19-2.333.80.14338280.71100
2.33-2.513.80.11638770.766100
2.51-2.763.80.09238740.85799.9
2.76-3.163.80.0738541.076100
3.16-3.993.80.05138951.47999.9
3.99-503.70.04139561.6699.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WC4

3wc4


Resolution: 1.851→26.235 Å / FOM work R set: 0.8926 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 1930 5 %Random selection
Rwork0.1513 36615 --
obs0.1531 38545 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.71 Å2 / Biso mean: 16.48 Å2 / Biso min: 4.24 Å2
Refinement stepCycle: final / Resolution: 1.851→26.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 41 486 3964
Biso mean--22.5 25.7 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063622
X-RAY DIFFRACTIONf_angle_d1.1324951
X-RAY DIFFRACTIONf_chiral_restr0.071581
X-RAY DIFFRACTIONf_plane_restr0.005633
X-RAY DIFFRACTIONf_dihedral_angle_d14.5881335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8507-1.89690.27661280.21172489X-RAY DIFFRACTION95
1.8969-1.94820.24511400.18532582X-RAY DIFFRACTION99
1.9482-2.00550.21211370.17012612X-RAY DIFFRACTION100
2.0055-2.07020.20821430.15712608X-RAY DIFFRACTION100
2.0702-2.14420.19231270.14092620X-RAY DIFFRACTION100
2.1442-2.230.1781190.1492615X-RAY DIFFRACTION100
2.23-2.33140.20281450.15052618X-RAY DIFFRACTION100
2.3314-2.45430.19781390.15112619X-RAY DIFFRACTION100
2.4543-2.60790.19141620.15342597X-RAY DIFFRACTION100
2.6079-2.8090.20491320.15712633X-RAY DIFFRACTION100
2.809-3.09130.18291240.15712654X-RAY DIFFRACTION100
3.0913-3.53770.18241330.14552647X-RAY DIFFRACTION100
3.5377-4.45360.15561460.1282626X-RAY DIFFRACTION100
4.4536-26.23720.16531550.14992695X-RAY DIFFRACTION99
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)
10.6381-0.04790.29511.1266-0.3230.8696-0.0015-0.0057-0.0314-0.0283-0.0131-0.03760.01870.00830.02120.0480.0030.02380.0666-0.0110.04845.71166.245215.7931
21.30030.9807-0.20741.3274-0.17640.4111-0.00630.0039-0.01820.07040.05830.03090.0132-0.0107-0.04490.07430.0347-0.00710.0772-0.0030.0687-5.7538-7.785631.9066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 249 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 250 through 446 )A0

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