[English] 日本語
Yorodumi
- PDB-7zer: Crystal structure of UGT85B1 from Sorghum bicolor in complex with UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zer
TitleCrystal structure of UGT85B1 from Sorghum bicolor in complex with UDP
ComponentsCyanohydrin beta-glucosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / cyanogenic / dhurrin biosynthesis / GT-B fold
Function / homology
Function and homology information


cyanohydrin beta-glucosyltransferase / dhurrin biosynthetic process / cyanohydrin beta-glucosyltransferase activity / endoplasmic reticulum membrane
Similarity search - Function
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
URIDINE-5'-DIPHOSPHATE / UDP-glucose:p-hydroxymandelonitrile O-glucosyltransferase
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsPutkaradze, N. / Fredslund, F. / Welner, D.H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20CC0035580 Denmark
Citation
Journal: Plant J. / Year: 2022
Title: Structure-guided engineering of key amino acids in UGT85B1 controlling substrate and stereo-specificity in aromatic cyanogenic glucoside biosynthesis.
Authors: Del Giudice, R. / Putkaradze, N. / Dos Santos, B.M. / Hansen, C.C. / Crocoll, C. / Motawia, M.S. / Fredslund, F. / Laursen, T. / Welner, D.H.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Liebschner, D. / Afonine, P.V.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyanohydrin beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6379
Polymers53,7991
Non-polymers8398
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint13 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.900, 90.150, 92.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Cyanohydrin beta-glucosyltransferase / UDP-glucose-p-hydroxymandelonitrile glucosyltransferase


Mass: 53798.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: UGT85B1, HMNGT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SBL1, cyanohydrin beta-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 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES/imidazole, 12.5% (w/v) PEG8000, 12.5% (v/v) ethylene glycol, 120 mM MORPHEUS monosaccharides mix

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2020
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.42→45.07 Å / Num. obs: 121023 / % possible obs: 99.19 % / Redundancy: 5 % / Biso Wilson estimate: 22.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.84
Reflection shellResolution: 1.42→1.471 Å / Num. unique obs: 44070 / CC1/2: 0.426

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UGT85H2

Resolution: 1.42→45.07 Å / SU ML: 0.1936 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1966 5932 4.9 %
Rwork0.1825 115091 -
obs0.1832 121023 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.87 Å2
Refinement stepCycle: LAST / Resolution: 1.42→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3599 0 53 327 3979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843726
X-RAY DIFFRACTIONf_angle_d0.97265064
X-RAY DIFFRACTIONf_chiral_restr0.0716571
X-RAY DIFFRACTIONf_plane_restr0.0106656
X-RAY DIFFRACTIONf_dihedral_angle_d14.0481339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.430.35751480.39882845X-RAY DIFFRACTION73.97
1.43-1.450.38441830.37493626X-RAY DIFFRACTION93.38
1.45-1.470.34871870.33573643X-RAY DIFFRACTION95.3
1.47-1.490.32442070.30683799X-RAY DIFFRACTION98.43
1.49-1.510.28851840.27733871X-RAY DIFFRACTION99.9
1.51-1.530.28212070.26373824X-RAY DIFFRACTION99.98
1.53-1.550.2452060.24133829X-RAY DIFFRACTION99.98
1.55-1.570.27231780.23613905X-RAY DIFFRACTION99.95
1.57-1.60.25862060.21653819X-RAY DIFFRACTION100
1.6-1.620.22551920.21463866X-RAY DIFFRACTION99.93
1.62-1.650.22711930.20223863X-RAY DIFFRACTION99.95
1.65-1.680.19462050.19063845X-RAY DIFFRACTION99.83
1.68-1.710.20772200.19183835X-RAY DIFFRACTION99.98
1.71-1.750.18861890.18453917X-RAY DIFFRACTION99.76
1.75-1.780.22581930.19173806X-RAY DIFFRACTION99.88
1.78-1.830.2032060.18743894X-RAY DIFFRACTION99.93
1.83-1.870.23282040.20493858X-RAY DIFFRACTION99.88
1.87-1.920.23422010.19663868X-RAY DIFFRACTION99.9
1.92-1.980.2051910.18683893X-RAY DIFFRACTION99.88
1.98-2.040.19612030.17753864X-RAY DIFFRACTION99.93
2.04-2.120.18091810.1773918X-RAY DIFFRACTION99.9
2.12-2.20.18862060.1743886X-RAY DIFFRACTION99.98
2.2-2.30.18642070.17273856X-RAY DIFFRACTION99.93
2.3-2.420.19692100.17043913X-RAY DIFFRACTION99.85
2.42-2.570.17092370.16943897X-RAY DIFFRACTION99.9
2.57-2.770.1942240.16773857X-RAY DIFFRACTION99.8
2.77-3.050.18081640.17643970X-RAY DIFFRACTION99.76
3.05-3.490.20771920.18713990X-RAY DIFFRACTION99.71
3.49-4.40.17021890.16093989X-RAY DIFFRACTION99.5
4.4-45.070.17922190.17074145X-RAY DIFFRACTION99.48

+
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