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- PDB-6ijd: Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with ... -

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Basic information

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


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 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,5,7,3',4'-PENTAHYDROXYFLAVONE / Flavonol 7-O-rhamnosyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.206 Å
AuthorsZong, G. / Wang, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China2017YFA0504801 China
National Natural Science Foundation of China15JCZDJC65500 China
CitationJournal: Plant J. / Year: 2019
Title: Crystal structures of rhamnosyltransferase UGT89C1 from Arabidopsis thaliana reveal the molecular basis of sugar donor specificity for UDP-beta-l-rhamnose and rhamnosylation mechanism.
Authors: Zong, G. / Fei, S. / Liu, X. / Li, J. / Gao, Y. / Yang, X. / Wang, X. / Shen, Y.
History
DepositionOct 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,9614
Polymers96,3562
Non-polymers6042
Water41423
1
A: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4802
Polymers48,1781
Non-polymers3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-8 kcal/mol
Surface area17690 Å2
MethodPISA
2
B: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4802
Polymers48,1781
Non-polymers3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-8 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.100, 81.100, 341.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 271 or (resid 272...
21(chain B and (resid 7 through 49 or (resid 50...

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
11LYSLYSVALVAL(chain A and (resid 7 through 271 or (resid 272...AA7 - 2717 - 271
12ARGARGARGARG(chain A and (resid 7 through 271 or (resid 272...AA272272
13LYSLYSLEULEU(chain A and (resid 7 through 271 or (resid 272...AA7 - 4357 - 435
14LYSLYSLEULEU(chain A and (resid 7 through 271 or (resid 272...AA7 - 4357 - 435
15LYSLYSLEULEU(chain A and (resid 7 through 271 or (resid 272...AA7 - 4357 - 435
16LYSLYSLEULEU(chain A and (resid 7 through 271 or (resid 272...AA7 - 4357 - 435
21LYSLYSSERSER(chain B and (resid 7 through 49 or (resid 50...BB7 - 497 - 49
22TYRTYRTYRTYR(chain B and (resid 7 through 49 or (resid 50...BB5050
23LYSLYSLEULEU(chain B and (resid 7 through 49 or (resid 50...BB7 - 4357 - 435
24LYSLYSLEULEU(chain B and (resid 7 through 49 or (resid 50...BB7 - 4357 - 435
25LYSLYSLEULEU(chain B and (resid 7 through 49 or (resid 50...BB7 - 4357 - 435
26LYSLYSLEULEU(chain B and (resid 7 through 49 or (resid 50...BB7 - 4357 - 435

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Components

#1: Protein UDP-glycosyltransferase 89C1 / rhamnosyltransferase UGT89C1


Mass: 48178.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UGT89C1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LNE6, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.78 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.8M potassium phosphate dibasic and 0.8M sodium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 17964 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Χ2: 0.921 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.265.50.7348930.9270.3270.8060.90699.4
3.26-3.316.10.7118880.9110.3060.7760.91999.1
3.31-3.386.50.5869170.9530.2460.6370.92399.7
3.38-3.4570.6018700.9530.2440.6490.95199.5
3.45-3.5270.5359090.9640.2160.5770.94699.7
3.52-3.670.4178960.9810.1690.450.94299.7
3.6-3.6970.3088990.9910.1250.3330.9699.7
3.69-3.7970.2568750.9920.1030.2760.96499.5
3.79-3.9170.2248970.9920.0910.2420.9899.8
3.91-4.036.80.1689030.9950.0690.1820.98799.8
4.03-4.186.60.1479010.9950.0610.1590.96799.8
4.18-4.346.30.1128860.9980.0480.1220.94499.9
4.34-4.545.80.0859140.9980.0380.0940.96399.7
4.54-4.785.70.0829080.9950.0380.0910.98899.6
4.78-5.086.60.0718820.9980.030.0770.94499.5
5.08-5.477.40.0759100.9980.030.0810.89499.8
5.47-6.027.40.078820.9980.0280.0760.87399.8
6.02-6.897.20.0629050.9980.0250.0670.863100
6.89-8.676.80.0299060.9990.0120.0310.793100
8-106.20.0159230.9990.0060.0160.73199.8

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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: 3.206→40.55 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.56
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2771 821 5.09 %
Rwork0.2021 --
obs0.2057 16137 89.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.78 Å2 / Biso mean: 54.1573 Å2 / Biso min: 19.22 Å2
Refinement stepCycle: final / Resolution: 3.206→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6274 0 44 23 6341
Biso mean--39.81 44.31 -
Num. residues----804
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3574X-RAY DIFFRACTION10.078TORSIONAL
12B3574X-RAY DIFFRACTION10.078TORSIONAL

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