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- PDB-6llg: Crystal Structure of Fagopyrum esculentum M UGT708C1 -

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Basic information

Entry
Database: PDB / ID: 6llg
TitleCrystal Structure of Fagopyrum esculentum M UGT708C1
ComponentsUDP-glycosyltransferase 708C1
KeywordsTRANSFERASE / C-glycosides / C-glucosyltransferases / crystal structures / catalytic mechanism
Function / homology2-hydroxyflavanone C-glucosyltransferase / UDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / BENZAMIDINE / UDP-glycosyltransferase 708C1
Function and homology information
Biological speciesFagopyrum esculentum (common buckwheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, X. / Liu, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504801 China
National Basic Research Program of China (973 Program)2018YFA0901800 China
CitationJournal: Plant Cell / Year: 2020
Title: Crystal Structures of theC-Glycosyltransferase UGT708C1 from Buckwheat Provide Insights into the Mechanism ofC-Glycosylation.
Authors: Liu, M. / Wang, D. / Li, Y. / Li, X. / Zong, G. / Fei, S. / Yang, X. / Lin, J. / Wang, X. / Shen, Y.
History
DepositionDec 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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: UDP-glycosyltransferase 708C1
B: UDP-glycosyltransferase 708C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4598
Polymers100,8592
Non-polymers6006
Water5,891327
1
A: UDP-glycosyltransferase 708C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6223
Polymers50,4291
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18910 Å2
MethodPISA
2
B: UDP-glycosyltransferase 708C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8385
Polymers50,4291
Non-polymers4084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.745, 144.247, 69.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-763-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 18 through 166 or (resid 167...
21(chain B and (resid 18 through 250 or (resid 251...

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
11ASPASPALAALA(chain A and (resid 18 through 166 or (resid 167...AA18 - 16618 - 166
12LYSLYSLYSLYS(chain A and (resid 18 through 166 or (resid 167...AA167167
13ASPASPARGARG(chain A and (resid 18 through 166 or (resid 167...AA18 - 45718 - 457
14ASPASPARGARG(chain A and (resid 18 through 166 or (resid 167...AA18 - 45718 - 457
15ASPASPARGARG(chain A and (resid 18 through 166 or (resid 167...AA18 - 45718 - 457
16ASPASPARGARG(chain A and (resid 18 through 166 or (resid 167...AA18 - 45718 - 457
21ASPASPASNASN(chain B and (resid 18 through 250 or (resid 251...BB18 - 25018 - 250
22GLUGLUGLUGLU(chain B and (resid 18 through 250 or (resid 251...BB251251
23ASPASPARGARG(chain B and (resid 18 through 250 or (resid 251...BB18 - 45718 - 457
24ASPASPARGARG(chain B and (resid 18 through 250 or (resid 251...BB18 - 45718 - 457
25ASPASPARGARG(chain B and (resid 18 through 250 or (resid 251...BB18 - 45718 - 457
26ASPASPARGARG(chain B and (resid 18 through 250 or (resid 251...BB18 - 45718 - 457

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Components

#1: Protein UDP-glycosyltransferase 708C1 / C-glucosyltransferase a / FeCGTa / UDP-glucose:2-hydroxyflavanone C-glucosyltransferase


Mass: 50429.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fagopyrum esculentum (common buckwheat)
Gene: UGT708C1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A1HA03, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 7.0, 26.5% (w/v) polyethylene glycol 5000, 20% (w/v) benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 58782 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.049 / Rrim(I) all: 0.124 / Χ2: 0.844 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.60.62328960.8860.260.6760.49299.8
2.14-2.186.50.55528790.9020.2330.6030.5199.6
2.18-2.226.50.50529200.920.2130.5490.53599.6
2.22-2.266.20.6728860.8530.290.7311.29299.3
2.26-2.315.80.41129100.9340.1840.4520.6599.6
2.31-2.376.50.35929090.9490.1510.390.67199.9
2.37-2.426.70.32129220.9540.1330.3480.70699.8
2.42-2.496.70.26529150.9670.1090.2870.64799.8
2.49-2.566.60.25428920.9680.1060.2750.73599.7
2.56-2.656.50.21129270.9790.0890.230.7499.5
2.65-2.746.40.1929190.9760.0810.2070.82599.4
2.74-2.855.90.16629270.9830.0730.1820.79699.5
2.85-2.986.70.14929390.9850.0610.1610.845100
2.98-3.146.70.13329690.9880.0550.1440.9399.7
3.14-3.336.60.11329410.990.0470.1220.99699.6
3.33-3.596.30.10329250.990.0450.1131.12799.1
3.59-3.956.20.0929540.9920.0390.0981.03598.8
3.95-4.526.50.08429880.9930.0360.0911.06499.6
4.52-5.760.0830100.9920.0360.0881.13698.7
5.7-506.10.07531540.9950.0330.0831.17298.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACV

2acv


Resolution: 2.1→33.963 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.78
RfactorNum. reflection% reflection
Rfree0.2112 1998 3.4 %
Rwork0.1738 --
obs0.1751 58684 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.62 Å2 / Biso mean: 47.4101 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.1→33.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6745 0 34 327 7106
Biso mean--79.66 47.78 -
Num. residues----870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086961
X-RAY DIFFRACTIONf_angle_d1.1179479
X-RAY DIFFRACTIONf_chiral_restr0.0611061
X-RAY DIFFRACTIONf_plane_restr0.0071215
X-RAY DIFFRACTIONf_dihedral_angle_d6.434141
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3976X-RAY DIFFRACTION10.405TORSIONAL
12B3976X-RAY DIFFRACTION10.405TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15120.28261370.2248389797
2.1512-2.20930.22381410.20734004100
2.2093-2.27430.30081410.2112400299
2.2743-2.34770.26111410.19974007100
2.3477-2.43160.24681430.194027100
2.4316-2.52890.26481420.19174034100
2.5289-2.6440.25281410.18424035100
2.644-2.78330.19611430.183401699
2.7833-2.95760.24341430.1874073100
2.9576-3.18580.23391440.18944089100
3.1858-3.50610.19321430.1808405299
3.5061-4.01280.20851430.1603407099
4.0128-5.0530.16961470.1426412799
5.053-33.9630.18741490.1649425398
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)
11.22070.09090.55661.5225-0.21343.37510.0821-0.0164-0.05680.04330.0325-0.0513-0.0424-0.0225-0.09470.29680.01860.01560.24280.00090.2865-13.257536.4878-22.4233
20.60690.0923-0.24096.24670.24911.2862-0.0004-0.0658-0.1020.13570.0761-0.34820.06480.1451-0.05620.26990.0193-0.00470.3150.00190.2612-11.595316.9291-37.4862
32.2244-0.40250.7842.08370.75573.3330.0109-0.0265-0.179-0.0089-0.04350.26090.106-0.26630.01730.2646-0.0339-0.030.23420.02130.243517.328222.1796-12.8859
42.2496-0.1391.2712.8862-0.16163.60360.09570.3466-0.1744-0.1155-0.0079-0.54030.17810.5858-0.11450.26410.0030.00820.3774-0.01610.384237.499318.2336-8.198
52.13531.8615-0.59886.44640.59851.103-0.0860.2234-0.1149-0.3545-0.0160.33850.0273-0.2570.11510.4498-0.0236-0.06410.3770.00040.288214.6873-2.60893.717
61.25621.08080.03297.26570.44060.79590.0725-0.1183-0.20410.1194-0.1152-0.15950.14360.05650.01060.3378-0.0128-0.05310.31860.01770.250728.46778.60237.0382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 245 )A18 - 245
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 457 )A246 - 457
3X-RAY DIFFRACTION3chain 'B' and (resid 18 through 139 )B18 - 139
4X-RAY DIFFRACTION4chain 'B' and (resid 140 through 245 )B140 - 245
5X-RAY DIFFRACTION5chain 'B' and (resid 246 through 360 )B246 - 360
6X-RAY DIFFRACTION6chain 'B' and (resid 361 through 457 )B361 - 457

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