[English] 日本語
Yorodumi
- PDB-4rem: Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltrans... -

+
Open data


ID or keywords:

Loading...

-
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-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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more