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Basic information

Entry
Database: PDB / ID: 6ija
TitleCrystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP-L-rhamnose
ComponentsUDP-glycosyltransferase 89C1
KeywordsPLANT PROTEIN / Arabidopsis thaliana / rhamnoside / rhamnosyltransferases
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
Chem-AWU / Flavonol 7-O-rhamnosyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.214 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)193,8136
Polymers192,7124
Non-polymers1,1012
Water50428
1
A: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7282
Polymers48,1781
Non-polymers5501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glycosyltransferase 89C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7282
Polymers48,1781
Non-polymers5501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-glycosyltransferase 89C1


Theoretical massNumber of molelcules
Total (without water)48,1781
Polymers48,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-glycosyltransferase 89C1


Theoretical massNumber of molelcules
Total (without water)48,1781
Polymers48,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.671, 84.983, 125.472
Angle α, β, γ (deg.)90.000, 89.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 214 or resid 231...
21(chain B and (resid 6 through 214 or resid 231...
31(chain C and (resid 6 through 214 or resid 231...
41(chain D and (resid 6 through 240 or resid 245...

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
11THRTHRLYSLYS(chain A and (resid 6 through 214 or resid 231...AA6 - 2146 - 214
12SERSERASPASP(chain A and (resid 6 through 214 or resid 231...AA231 - 240231 - 240
13TYRTYRTYRTYR(chain A and (resid 6 through 214 or resid 231...AA245245
14THRTHRLEULEU(chain A and (resid 6 through 214 or resid 231...AA5 - 4355 - 435
15THRTHRLEULEU(chain A and (resid 6 through 214 or resid 231...AA5 - 4355 - 435
16THRTHRLEULEU(chain A and (resid 6 through 214 or resid 231...AA5 - 4355 - 435
17THRTHRLEULEU(chain A and (resid 6 through 214 or resid 231...AA5 - 4355 - 435
18THRTHRLEULEU(chain A and (resid 6 through 214 or resid 231...AA5 - 4355 - 435
19THRTHRLEULEU(chain A and (resid 6 through 214 or resid 231...AA5 - 4355 - 435
21THRTHRLYSLYS(chain B and (resid 6 through 214 or resid 231...BB6 - 2146 - 214
22SERSERASPASP(chain B and (resid 6 through 214 or resid 231...BB231 - 240231 - 240
23TYRTYRGLUGLU(chain B and (resid 6 through 214 or resid 231...BB245 - 257245 - 257
24GLNGLNGLNGLN(chain B and (resid 6 through 214 or resid 231...BB258258
25THRTHRLEULEU(chain B and (resid 6 through 214 or resid 231...BB6 - 4356 - 435
26THRTHRLEULEU(chain B and (resid 6 through 214 or resid 231...BB6 - 4356 - 435
27THRTHRLEULEU(chain B and (resid 6 through 214 or resid 231...BB6 - 4356 - 435
28THRTHRLEULEU(chain B and (resid 6 through 214 or resid 231...BB6 - 4356 - 435
31THRTHRLYSLYS(chain C and (resid 6 through 214 or resid 231...CC6 - 2146 - 214
32SERSERLEULEU(chain C and (resid 6 through 214 or resid 231...CC231 - 339231 - 339
33GLUGLUGLUGLU(chain C and (resid 6 through 214 or resid 231...CC340340
34THRTHRLEULEU(chain C and (resid 6 through 214 or resid 231...CC6 - 4356 - 435
35THRTHRLEULEU(chain C and (resid 6 through 214 or resid 231...CC6 - 4356 - 435
36THRTHRLEULEU(chain C and (resid 6 through 214 or resid 231...CC6 - 4356 - 435
37THRTHRLEULEU(chain C and (resid 6 through 214 or resid 231...CC6 - 4356 - 435
41THRTHRASPASP(chain D and (resid 6 through 240 or resid 245...DD6 - 2406 - 240
42TYRTYRGLUGLU(chain D and (resid 6 through 240 or resid 245...DD245 - 257245 - 257
43GLNGLNGLNGLN(chain D and (resid 6 through 240 or resid 245...DD258258
44THRTHRLEULEU(chain D and (resid 6 through 240 or resid 245...DD6 - 4356 - 435
45THRTHRLEULEU(chain D and (resid 6 through 240 or resid 245...DD6 - 4356 - 435
46THRTHRLEULEU(chain D and (resid 6 through 240 or resid 245...DD6 - 4356 - 435
47THRTHRLEULEU(chain D and (resid 6 through 240 or resid 245...DD6 - 4356 - 435

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Components

#1: Protein
UDP-glycosyltransferase 89C1 / UDP-rhamnose: flavonol 7-O-rhamnosyltransferase


Mass: 48178.086 Da / Num. of mol.: 4
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-AWU / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 550.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.97 %
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: NFPSS / Beamline: BL18U / Wavelength: 0.97891 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 24, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 31198 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Χ2: 0.956 / Net I/σ(I): 6 / Num. measured all: 210757
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.3170.77531000.7770.3150.8370.846100
3.31-3.456.80.52730900.8670.2160.570.87699.8
3.45-3.66.40.35530900.9360.1510.3860.91699.8
3.6-3.796.50.24131010.9620.1020.2620.97199.7
3.79-4.037.20.16931160.9840.0680.1831.052100
4.03-4.347.10.1230900.9890.0480.1291.066100
4.34-4.786.90.09331490.9930.0380.1011.056100
4.78-5.476.20.07630980.9950.0330.0830.95899.5
5.47-6.8970.06731510.9970.0270.0720.918100
6.89-506.50.03332130.9970.0140.0360.88999.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IJ7

6ij7


Resolution: 3.214→45.335 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2907 1509 4.98 %
Rwork0.2159 28779 -
obs0.2196 30288 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.4 Å2 / Biso mean: 56.7476 Å2 / Biso min: 14.98 Å2
Refinement stepCycle: final / Resolution: 3.214→45.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12554 0 70 28 12652
Biso mean--48.89 39.78 -
Num. residues----1603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112942
X-RAY DIFFRACTIONf_angle_d1.3717608
X-RAY DIFFRACTIONf_chiral_restr0.0682022
X-RAY DIFFRACTIONf_plane_restr0.0082224
X-RAY DIFFRACTIONf_dihedral_angle_d5.4627745
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6990X-RAY DIFFRACTION14.389TORSIONAL
12B6990X-RAY DIFFRACTION14.389TORSIONAL
13C6990X-RAY DIFFRACTION14.389TORSIONAL
14D6990X-RAY DIFFRACTION14.389TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2139-3.31760.40351140.30241952206674
3.3176-3.43610.34831330.27472567270095
3.4361-3.57360.3251220.25442628275098
3.5736-3.73620.30871320.23752670280299
3.7362-3.93310.28761500.218227042854100
3.9331-4.17930.26031360.203227012837100
4.1793-4.50170.29831280.192627172845100
4.5017-4.95430.27111340.186227012835100
4.9543-5.670.27351580.2072712287099
5.67-7.13910.34081500.241527122862100
7.1391-45.33990.23731520.18352715286798

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