[English] 日本語
Yorodumi
- PDB-8i94: Structure of flavone 4'-O-glucoside 7-O-glucosyltransferase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i94
TitleStructure of flavone 4'-O-glucoside 7-O-glucosyltransferase from Nemophila menziesii, complex with luteolin
ComponentsGlycosyltransferase
KeywordsPLANT PROTEIN / flavone / luteolin
Function / homologyUDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / Chem-LU2 / Glycosyltransferase
Function and homology information
Biological speciesNemophila menziesii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Shirouzu, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Molecular basis of ligand recognition specificity of flavone glucosyltransferases in Nemophila menziesii.
Authors: Murayama, K. / Kato-Murayama, M. / Hosaka, T. / Okitsu, N. / Tanaka, Y. / Shirouzu, M.
History
DepositionFeb 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5256
Polymers108,7602
Non-polymers7654
Water1,63991
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7623
Polymers54,3801
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19580 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7623
Polymers54,3801
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.975, 75.226, 119.743
Angle α, β, γ (deg.)90.000, 96.497, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Glycosyltransferase


Mass: 54380.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nemophila menziesii (plant) / Gene: NmF4'G7GT / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A292GEP7, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-LU2 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one / Luteolin


Mass: 286.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, Hepes, Lithium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.43→48.33 Å / Num. obs: 35086 / % possible obs: 94.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.33 Å2 / Rrim(I) all: 0.222 / Net I/σ(I): 7.4
Reflection shellResolution: 2.43→2.52 Å / Num. unique obs: 3377 / CC1/2: 0.85

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→48.33 Å / SU ML: 0.3962 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 35.2474 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.3094 1999 5.7 %
Rwork0.2373 33064 -
obs0.2415 35063 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.38 Å2
Refinement stepCycle: LAST / Resolution: 2.43→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6942 0 52 91 7085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857157
X-RAY DIFFRACTIONf_angle_d1.02039703
X-RAY DIFFRACTIONf_chiral_restr0.05391079
X-RAY DIFFRACTIONf_plane_restr0.0071232
X-RAY DIFFRACTIONf_dihedral_angle_d3.5834320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.490.36641260.29312094X-RAY DIFFRACTION84
2.49-2.560.36761450.26572388X-RAY DIFFRACTION95.58
2.56-2.630.37661460.27412395X-RAY DIFFRACTION95.92
2.63-2.720.35491410.28492346X-RAY DIFFRACTION93.99
2.72-2.820.34591430.25522371X-RAY DIFFRACTION93.84
2.82-2.930.34091440.25132361X-RAY DIFFRACTION94.17
2.93-3.060.30631380.24772311X-RAY DIFFRACTION92.91
3.06-3.220.36921410.25792325X-RAY DIFFRACTION92.67
3.22-3.430.38811400.24382326X-RAY DIFFRACTION92.19
3.43-3.690.29471380.23012286X-RAY DIFFRACTION91.4
3.69-4.060.28471420.2132333X-RAY DIFFRACTION92.39
4.06-4.650.2621460.20082416X-RAY DIFFRACTION95.14
4.65-5.860.27011530.21922518X-RAY DIFFRACTION99.44
5.86-48.330.28471560.24872594X-RAY DIFFRACTION99.67

+
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