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- PDB-6ij9: Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP -

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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


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
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
Revision 1.2Oct 9, 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)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

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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


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


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.48 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

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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

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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→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

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