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- PDB-6ij7: Crystal Structure of Arabidopsis thaliana UGT89C1 -

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Basic information

Entry
Database: PDB / ID: 6ij7
TitleCrystal Structure of Arabidopsis thaliana UGT89C1
ComponentsRhamnosyltransferase protein
KeywordsPLANT PROTEIN / Arabidopsis thaliana / rhamnosyltransferase / rhamnoside
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
Flavonol 7-O-rhamnosyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsZong, G. / Wang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China2017YFA0504801 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

Downloads & links

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Assembly

Deposited unit
A: Rhamnosyltransferase protein
B: Rhamnosyltransferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,15913
Polymers96,3562
Non-polymers80311
Water63135
1
A: Rhamnosyltransferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7038
Polymers48,1781
Non-polymers5257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint0 kcal/mol
Surface area17700 Å2
MethodPISA
2
B: Rhamnosyltransferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4565
Polymers48,1781
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.647, 80.647, 340.192
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 213 or resid 223 through 435))
21(chain B and (resid 7 through 213 or resid 223...

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
11LYSLYSPHEPHE(chain A and (resid 7 through 213 or resid 223 through 435))AA7 - 2137 - 213
12SERSERLEULEU(chain A and (resid 7 through 213 or resid 223 through 435))AA223 - 435223 - 435
21LYSLYSPHEPHE(chain B and (resid 7 through 213 or resid 223...BB7 - 2137 - 213
22SERSERVALVAL(chain B and (resid 7 through 213 or resid 223...BB223 - 277223 - 277
23PROPROPROPRO(chain B and (resid 7 through 213 or resid 223...BB297297
24LYSLYSLEULEU(chain B and (resid 7 through 213 or resid 223...BB7 - 4357 - 435
25LYSLYSLEULEU(chain B and (resid 7 through 213 or resid 223...BB7 - 4357 - 435
26LYSLYSLEULEU(chain B and (resid 7 through 213 or resid 223...BB7 - 4357 - 435
27LYSLYSLEULEU(chain B and (resid 7 through 213 or resid 223...BB7 - 4357 - 435
28LYSLYSLEULEU(chain B and (resid 7 through 213 or resid 223...BB7 - 4357 - 435

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Components

#1: Protein Rhamnosyltransferase protein


Mass: 48178.086 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 35 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M ammonium sulfate, 0.1M sodium cacodylate pH 6.0, 25%(w/v) PEG8000 and 3%(v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 29577 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.049 / Rrim(I) all: 0.129 / Χ2: 0.816 / Net I/σ(I): 4.2 / Num. measured all: 199886
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.85.70.57129510.9020.2530.6260.51299.5
2.8-2.916.60.51829420.9260.2170.5620.524100
2.91-3.046.80.39229370.9530.1620.4240.581100
3.04-3.26.50.28929630.9670.1220.3140.66100
3.2-3.47.20.21629520.9830.0870.2320.735100
3.4-3.667.10.15829860.9870.0640.1710.877100
3.66-4.036.80.11829420.9890.0490.1271.055100
4.03-4.6270.09629530.9940.0390.1041.069100
4.62-5.8170.08929680.9930.0360.0961.032100
5.81-106.70.07229830.9960.0310.0791.025100

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACV

2acv


Resolution: 2.701→47.364 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.46
RfactorNum. reflection% reflection
Rfree0.26 1498 5.08 %
Rwork0.2175 --
obs0.2196 29494 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.15 Å2 / Biso mean: 66.9422 Å2 / Biso min: 36.85 Å2
Refinement stepCycle: final / Resolution: 2.701→47.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6324 0 52 35 6411
Biso mean--59.89 57.1 -
Num. residues----807
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3750X-RAY DIFFRACTION9.209TORSIONAL
12B3750X-RAY DIFFRACTION9.209TORSIONAL
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.683-0.46470.31983.106-0.9893.7547-0.0357-0.47230.15880.33380.02340.13340.0078-0.09450.00260.2853-0.01420.05930.5368-0.06610.355522.9256-11.89475.5236
23.7193-2.5005-1.42351.93740.43063.350.292-1.26050.64410.68790.06420.76470.00960.204-0.34360.8939-0.02530.01340.8281-0.31951.394622.498418.27961.3389
33.69651.12961.04373.04040.47221.45570.1238-1.11311.83930.69210.27660.9308-1.3881-0.6361-0.06260.77890.08640.12610.9089-0.26721.02511.740421.24544.1144
43.47480.8835-0.38065.44260.45422.6340.03910.31420.7791-0.30310.03670.8736-0.2613-0.526-0.09560.30950.05760.00410.52-0.02150.498316.99262.5646-8.387
53.5856-0.46420.64193.01910.14155.4738-0.07210.55320.0364-0.45980.031-0.0405-0.1919-0.17730.03280.48230.00780.02180.292-0.03850.331125.7763-15.1625-45.6877
64.9135-0.4102-0.02392.98970.52182.72350.04110.1494-0.5996-0.10370.0043-0.81410.46250.3133-0.05810.60560.04660.07340.30130.00350.567745.4453-23.8143-32.7705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 246 )A7 - 246
2X-RAY DIFFRACTION2chain 'A' and (resid 247 through 269 )A247 - 269
3X-RAY DIFFRACTION3chain 'A' and (resid 270 through 313 )A270 - 313
4X-RAY DIFFRACTION4chain 'A' and (resid 314 through 435 )A314 - 435
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 187 )B7 - 187
6X-RAY DIFFRACTION6chain 'B' and (resid 188 through 435 )B188 - 435

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