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- PDB-6llw: Crystal Structure of Fagopyrum esculentum M UGT708C1 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6llw
TitleCrystal Structure of Fagopyrum esculentum M UGT708C1 complexed with UDP
ComponentsUDP-glycosyltransferase 708C1
KeywordsTRANSFERASE / C-glycosides / C-glucosyltransferases
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 / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 708C1
Function and homology information
Biological speciesFagopyrum esculentum (common buckwheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 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 1.0Aug 5, 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)101,6674
Polymers100,8592
Non-polymers8082
Water6,269348
1
A: UDP-glycosyltransferase 708C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8342
Polymers50,4291
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-9 kcal/mol
Surface area18600 Å2
MethodPISA
2
B: UDP-glycosyltransferase 708C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8342
Polymers50,4291
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-7 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.308, 144.105, 69.808
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
11A-1036-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 18 through 165 or resid 169...
21(chain B and (resid 18 through 338 or (resid 339...

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
11ASPASPLEULEU(chain A and (resid 18 through 165 or resid 169...AA18 - 16518 - 165
12SERSERASPASP(chain A and (resid 18 through 165 or resid 169...AA169 - 235169 - 235
13SERSERGLUGLU(chain A and (resid 18 through 165 or resid 169...AA238 - 253238 - 253
14GLNGLNLYSLYS(chain A and (resid 18 through 165 or resid 169...AA257 - 307257 - 307
15ASPASPLYSLYS(chain A and (resid 18 through 165 or resid 169...AA18 - 45618 - 456
16ASPASPLYSLYS(chain A and (resid 18 through 165 or resid 169...AA18 - 45618 - 456
17ASPASPLYSLYS(chain A and (resid 18 through 165 or resid 169...AA18 - 45618 - 456
18ASPASPLYSLYS(chain A and (resid 18 through 165 or resid 169...AA18 - 45618 - 456
19ASPASPLYSLYS(chain A and (resid 18 through 165 or resid 169...AA18 - 45618 - 456
21ASPASPVALVAL(chain B and (resid 18 through 338 or (resid 339...BB18 - 33818 - 338
22LYSLYSLYSLYS(chain B and (resid 18 through 338 or (resid 339...BB339339
23ASPASPLYSLYS(chain B and (resid 18 through 338 or (resid 339...BB18 - 45618 - 456
24ASPASPLYSLYS(chain B and (resid 18 through 338 or (resid 339...BB18 - 45618 - 456
25ASPASPLYSLYS(chain B and (resid 18 through 338 or (resid 339...BB18 - 45618 - 456
26ASPASPLYSLYS(chain B and (resid 18 through 338 or (resid 339...BB18 - 45618 - 456

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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-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 0.1M MES pH 7.0, 26.5%(w/v) polyethylene glycol 5000, 26%(w/v) benzamidine hydrochloride, 5mM UDP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 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: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 47227 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Χ2: 0.96 / Net I/σ(I): 13.6 / Num. measured all: 305071
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.295.90.24723140.9650.110.2711.05799.7
2.29-2.336.10.23623270.9730.1030.2581.04699.7
2.33-2.386.70.22123140.9750.0920.241.077100
2.38-2.426.60.19323440.9780.0810.2091.02899.9
2.42-2.486.70.17723340.9790.0740.1920.98399.9
2.48-2.536.60.17123350.9830.0720.1851.01399.8
2.53-2.66.60.15123420.9810.0640.1640.978100
2.6-2.676.40.1423700.9870.0590.1531.00599.9
2.67-2.756.40.13123190.9880.0560.1420.99199.7
2.75-2.835.90.11623070.9840.0510.1270.91998.8
2.83-2.946.80.11623700.9880.0480.1250.97399.9
2.94-3.056.80.10823560.9890.0450.1170.9599.9
3.05-3.196.70.10123430.990.0420.110.9399.9
3.19-3.366.60.09623630.9910.040.1040.93899.8
3.36-3.576.40.09323660.9880.040.1020.952100
3.57-3.856.30.09123720.9880.0390.10.92798.9
3.85-4.236.80.08923810.9910.0370.0960.89399.6
4.23-4.856.60.08924140.9850.0380.0970.90899.8
4.85-6.16.20.08524010.990.0370.0930.80398.5
6.1-506.20.08425550.9920.0360.0920.83798.8

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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: 2.256→40.19 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.66 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2152 2356 5.05 %
Rwork0.1705 44292 -
obs0.1727 46648 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.41 Å2 / Biso mean: 35.8397 Å2 / Biso min: 12.37 Å2
Refinement stepCycle: final / Resolution: 2.256→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 50 348 7040
Biso mean--40.61 39.63 -
Num. residues----857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086912
X-RAY DIFFRACTIONf_angle_d1.0689420
X-RAY DIFFRACTIONf_chiral_restr0.0661059
X-RAY DIFFRACTIONf_plane_restr0.0081203
X-RAY DIFFRACTIONf_dihedral_angle_d6.1254094
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3910X-RAY DIFFRACTION8.667TORSIONAL
12B3910X-RAY DIFFRACTION8.667TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.256-2.30170.24031270.1875218785
2.3017-2.35170.26181330.1862248194
2.3517-2.40640.25431390.1861258498
2.4064-2.46660.23031370.1855258299
2.4666-2.53320.2431440.18712605100
2.5332-2.60780.30561310.18062632100
2.6078-2.69190.20661150.18322634100
2.6919-2.78810.24561540.1786261499
2.7881-2.89970.22231230.1855262399
2.8997-3.03160.2321240.18742640100
3.0316-3.19140.23531380.18072642100
3.1914-3.39130.21151440.17692638100
3.3913-3.6530.20191470.1689263999
3.653-4.02030.1991500.15562643100
4.0203-4.60130.16551530.13762662100
4.6013-5.79440.21371550.1611267499
5.7944-40.190.20111420.1726281298
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)
11.2-0.07660.35721.6231-0.22594.01710.0031-0.0292-0.11530.0550.0277-0.0749-0.0884-0.0599-0.02760.14290.03280.00690.1442-0.00750.2104-12.874336.6029-22.4223
20.3636-0.0359-0.1825.220.23321.1556-0.0296-0.0407-0.09580.00350.1129-0.24160.02510.1146-0.07560.13260.01680.00850.23370.00930.186-11.496616.7218-37.461
31.7312-0.07171.09891.70150.21622.66940.05050.0776-0.1326-0.0376-0.0252-0.05730.04240.0736-0.00810.1518-0.0416-0.00370.15480.01540.1925.387219.9511-11.567
41.23521.21120.01533.8038-0.25050.7774-0.00750.0319-0.1537-0.0362-0.0582-0.05790.1212-0.00170.08080.2164-0.0135-0.02730.2132-0.00210.145422.68723.88034.9185
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 456 )A246 - 456
3X-RAY DIFFRACTION3chain 'B' and (resid 18 through 224 )B18 - 224
4X-RAY DIFFRACTION4chain 'B' and (resid 225 through 456 )B225 - 456

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