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

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Basic information

Entry
Database: PDB / ID: 4ren
TitleCrystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with petunidin
ComponentsUDP-glucose:anthocyanidin 3-O-glucosyltransferase
KeywordsTRANSFERASE / UGT78K6 / GT-B fold / Glucosyltransferase / Complexed with petunidin
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-P5M / Glycosyltransferase
Similarity search - Component
Biological speciesClitoria ternatea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 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)49,4636
Polymers48,7771
Non-polymers6865
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.903, 55.279, 85.801
Angle α, β, γ (deg.)90.00, 104.60, 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-P5M / 2-(3,4-dihydroxy-5-methoxyphenyl)-3,5,7-trihydroxychromenium / Petunidin


Mass: 317.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 47.61 % / Mosaicity: 0.886 °
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: 2.7→50 Å / Num. obs: 12456 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.75 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.531 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.83.80.40212521.55598.4
2.8-2.913.80.32812231.58698.8
2.91-3.043.80.26612161.5898.3
3.04-3.23.80.22212271.60598.7
3.2-3.43.80.14712561.68299.2
3.4-3.663.80.10612351.61799
3.66-4.033.80.07812341.55799.1
4.03-4.623.80.05412581.47199.3
4.62-5.813.70.05112541.35499.3
5.81-503.60.03713011.29599.1

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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: 2.704→46.014 Å / FOM work R set: 0.8432 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 610 4.9 %RANDAM
Rwork0.1816 ---
obs0.1844 12437 98.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.85 Å2 / Biso mean: 32.47 Å2 / Biso min: 13.32 Å2
Refinement stepCycle: LAST / Resolution: 2.704→46.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 47 75 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033589
X-RAY DIFFRACTIONf_angle_d0.7474888
X-RAY DIFFRACTIONf_chiral_restr0.05571
X-RAY DIFFRACTIONf_plane_restr0.003621
X-RAY DIFFRACTIONf_dihedral_angle_d12.641306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7038-2.97580.28941610.22932904306598
2.9758-3.40630.30881390.21512947308699
3.4063-4.29110.24571490.1712944309399
4.2911-46.02090.18311610.15363032319399
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)
10.27670.08040.30420.7742-0.43680.713-0.02010.02930.0020.027-0.0133-0.0439-0.01730.0138-00.1480.00620.00840.1723-0.02620.17026.70316.294215.2652
20.62490.4134-0.06960.2731-0.0540.120.00880.00330.0460.05440.01940.1491-0.04110.015200.2990.00770.01780.2311-0.00440.239-5.8441-6.664531.9117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 1 through 236 )A1 - 236
2X-RAY DIFFRACTION2chain A and (resid 237 through 446 )A237 - 446

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