[English] 日本語
Yorodumi
- PDB-6ij9: Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ij9
TitleCrystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP
ComponentsUDP-glycosyltransferase 89C1
KeywordsPLANT PROTEIN / Arabidopsis thaliana / rhamnoside / rhamnosyltransferases
Function / homology
Function and homology information


quercetin 3-glucoside 7-O-rhamnosyltransferase activity / quercetin 3-rhamnoside 7-O-rhamnosyltransferase activity / flavonol biosynthetic process / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / extracellular region / cytosol
Similarity search - Function
UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Flavonol 7-O-rhamnosyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZong, G.N. / Wang, X.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China2017YFA0504801 China
CitationJournal: To Be Published
Title: Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP
Authors: Zong, G.N. / Wang, X.Q.
History
DepositionOct 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glycosyltransferase 89C1
B: UDP-glycosyltransferase 89C1
C: UDP-glycosyltransferase 89C1
D: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,3298
Polymers192,7124
Non-polymers1,6174
Water1,09961
1
A: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5822
Polymers48,1781
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-9 kcal/mol
Surface area17180 Å2
MethodPISA
2
B: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5822
Polymers48,1781
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-9 kcal/mol
Surface area17330 Å2
MethodPISA
3
C: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5822
Polymers48,1781
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-8 kcal/mol
Surface area17690 Å2
MethodPISA
4
D: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5822
Polymers48,1781
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-9 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.979, 84.141, 129.146
Angle α, β, γ (deg.)90.000, 108.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 210 or (resid 211...
21(chain B and ((resid 8 and (name N or name...
31(chain C and ((resid 8 and (name N or name...
41(chain D and ((resid 8 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEU(chain A and (resid 8 through 210 or (resid 211...AA8 - 2108 - 210
12LEULEULEULEU(chain A and (resid 8 through 210 or (resid 211...AA211211
13LYSLYSLEULEU(chain A and (resid 8 through 210 or (resid 211...AA8 - 4358 - 435
21LYSLYSLYSLYS(chain B and ((resid 8 and (name N or name...BB88
22LYSLYSLEULEU(chain B and ((resid 8 and (name N or name...BB8 - 4358 - 435
23LYSLYSLEULEU(chain B and ((resid 8 and (name N or name...BB8 - 4358 - 435
24LYSLYSLEULEU(chain B and ((resid 8 and (name N or name...BB8 - 4358 - 435
25LYSLYSLEULEU(chain B and ((resid 8 and (name N or name...BB8 - 4358 - 435
31LYSLYSLYSLYS(chain C and ((resid 8 and (name N or name...CC88
32LYSLYSLEULEU(chain C and ((resid 8 and (name N or name...CC7 - 4357 - 435
33LYSLYSLEULEU(chain C and ((resid 8 and (name N or name...CC7 - 4357 - 435
34LYSLYSLEULEU(chain C and ((resid 8 and (name N or name...CC7 - 4357 - 435
35LYSLYSLEULEU(chain C and ((resid 8 and (name N or name...CC7 - 4357 - 435
41LYSLYSLYSLYS(chain D and ((resid 8 and (name N or name...DD88
42LYSLYSLEULEU(chain D and ((resid 8 and (name N or name...DD7 - 4357 - 435
43LYSLYSLEULEU(chain D and ((resid 8 and (name N or name...DD7 - 4357 - 435
44LYSLYSLEULEU(chain D and ((resid 8 and (name N or name...DD7 - 4357 - 435
45LYSLYSLEULEU(chain D and ((resid 8 and (name N or name...DD7 - 4357 - 435

-
Components

#1: Protein
UDP-glycosyltransferase 89C1


Mass: 48178.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LNE6, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M ammonium sulfate, 0.1M HEPES pH 7.5, 20%(w/v) PEG8000 and 10%(v/v) 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 39311 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.052 / Rrim(I) all: 0.098 / Χ2: 0.956 / Net I/σ(I): 6.1 / Num. measured all: 134011
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.113.40.61638770.8720.3870.730.997.4
3.11-3.233.40.45138500.9140.2840.5350.90998.2
3.23-3.383.40.31439550.9560.1970.3720.91499.3
3.38-3.563.40.23639230.9760.1490.280.95599.1
3.56-3.783.20.14738670.9880.0980.1781.02398.2
3.78-4.073.60.10439660.9940.0640.1220.96699.5
4.07-4.483.60.07639600.9960.0470.091.0499.4
4.48-5.133.40.06139430.9960.0380.0721.06599.1
5.13-6.463.30.05839470.9970.0370.0690.93598.6
6.46-103.30.03940230.9970.0250.0460.85198

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IJ7

6ij7


Resolution: 3→29.931 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.09
RfactorNum. reflection% reflection
Rfree0.2738 1574 4.99 %
Rwork0.2171 --
obs0.22 31568 83.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.93 Å2 / Biso mean: 40.5494 Å2 / Biso min: 13.26 Å2
Refinement stepCycle: final / Resolution: 3→29.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12643 0 100 61 12804
Biso mean--40.47 31.02 -
Num. residues----1619
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7065X-RAY DIFFRACTION12.674TORSIONAL
12B7065X-RAY DIFFRACTION12.674TORSIONAL
13C7065X-RAY DIFFRACTION12.674TORSIONAL
14D7065X-RAY DIFFRACTION12.674TORSIONAL

+
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