[English] 日本語
Yorodumi
- PDB-5u6m: Crystal structure of UDP-glucosyltransferase, UGT74F2, with UDP a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u6m
TitleCrystal structure of UDP-glucosyltransferase, UGT74F2, with UDP and salicylic acid
ComponentsUDP-glycosyltransferase 74F2
KeywordsTRANSFERASE / UDP-glucosyltransferase / salicylic acid / salicylic acid glucoside / salicylic acid ester
Function / homology
Function and homology information


para-aminobenzoic acid metabolic process / salicylic acid glucosyltransferase (ester-forming) activity / salicylic acid glucosyltransferase (glucoside-forming) activity / benzoic acid glucosyltransferase activity / UDP-glucose:4-aminobenzoate acylglucosyltransferase activity / nicotinate-O-glucosyltransferase activity / positive regulation of seed germination / benzoate metabolic process / salicylic acid metabolic process / UDP-glucosyltransferase activity ...para-aminobenzoic acid metabolic process / salicylic acid glucosyltransferase (ester-forming) activity / salicylic acid glucosyltransferase (glucoside-forming) activity / benzoic acid glucosyltransferase activity / UDP-glucose:4-aminobenzoate acylglucosyltransferase activity / nicotinate-O-glucosyltransferase activity / positive regulation of seed germination / benzoate metabolic process / salicylic acid metabolic process / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / cytosol
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
beta-D-glucopyranose / 2-HYDROXYBENZOIC ACID / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 74F2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.568 Å
AuthorsGeorge Thompson, A.M. / Iancu, C.V. / Dean, J.V. / Choe, J.
CitationJournal: Sci Rep / Year: 2017
Title: Differences in salicylic acid glucose conjugations by UGT74F1 and UGT74F2 from Arabidopsis thaliana.
Authors: George Thompson, A.M. / Iancu, C.V. / Neet, K.E. / Dean, J.V. / Choe, J.Y.
History
DepositionDec 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glycosyltransferase 74F2
B: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0888
Polymers101,6432
Non-polymers1,4456
Water905
1
A: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5444
Polymers50,8221
Non-polymers7223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5444
Polymers50,8221
Non-polymers7223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.694, 87.681, 164.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 UDP-glycosyltransferase 74F2 / AtSGT1 / Salicylic acid glucosyltransferase 1


Mass: 50821.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UGT74F2, GT, SAGT1, SGT1, At2g43820, F18O19.7 / Production host: Escherichia coli (E. coli)
References: UniProt: O22822, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22-26 % (w/v) PEG3350, 0.2 M ammonium acetate, 0.1 M MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 30702 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 68.6431469736 Å2 / Net I/σ(I): 0.086
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.7 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.568→43.841 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 1541 5.03 %
Rwork0.1876 --
obs0.1914 30628 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.568→43.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7060 0 92 5 7157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117334
X-RAY DIFFRACTIONf_angle_d1.2139965
X-RAY DIFFRACTIONf_dihedral_angle_d4.6484311
X-RAY DIFFRACTIONf_chiral_restr0.0621107
X-RAY DIFFRACTIONf_plane_restr0.0081264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5683-2.65120.36041240.2772428X-RAY DIFFRACTION93
2.6512-2.74590.34141390.26092618X-RAY DIFFRACTION99
2.7459-2.85580.36181500.25392601X-RAY DIFFRACTION99
2.8558-2.98580.37241300.24042633X-RAY DIFFRACTION99
2.9858-3.14320.30621380.23932629X-RAY DIFFRACTION99
3.1432-3.340.33251460.22862638X-RAY DIFFRACTION99
3.34-3.59780.32181250.21132652X-RAY DIFFRACTION100
3.5978-3.95960.23981450.18562654X-RAY DIFFRACTION99
3.9596-4.53210.2051400.15622694X-RAY DIFFRACTION100
4.5321-5.7080.24221500.16412709X-RAY DIFFRACTION100
5.708-43.84690.2241540.16512831X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 56.5102 Å / Origin y: 75.947 Å / Origin z: 59.1517 Å
111213212223313233
T0.4321 Å20.0634 Å20.0059 Å2-0.414 Å20.0224 Å2--0.5086 Å2
L0.4705 °20.0741 °2-0.6546 °2-0.4431 °20.4679 °2--2.0802 °2
S0.0443 Å °0.0206 Å °0.0454 Å °-0.0669 Å °0.0166 Å °0.035 Å °-0.0213 Å °-0.0763 Å °0.0136 Å °
Refinement TLS groupSelection details: all

+
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