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- PDB-7vel: Crystal structure of Phytolacca americana UGT3 with UDP-2fluoroglucose -

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Basic information

Entry
Database: PDB / ID: 7vel
TitleCrystal structure of Phytolacca americana UGT3 with UDP-2fluoroglucose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / UGT / glycosyltransferase / UDP-2FGlc
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / 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
: / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Chem-U2F / Glycosyltransferase
Similarity search - Component
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMaharjan, R. / Fukuda, Y. / Nakayama, T. / Nakayama, T. / Hamada, H. / Ozaki, S. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural basis for substrate recognition in the Phytolacca americana glycosyltransferase PaGT3.
Authors: Maharjan, R. / Fukuda, Y. / Nakayama, T. / Nakayama, T. / Hamada, H. / Ozaki, S.I. / Inoue, T.
History
DepositionSep 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7627
Polymers115,2602
Non-polymers1,5025
Water2,954164
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5645
Polymers57,6301
Non-polymers9344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-5 kcal/mol
Surface area19210 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1982
Polymers57,6301
Non-polymers5681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-4 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.218, 103.851, 110.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11GLNGLNGLUGLU(chain 'A' and resid 7 through 484)AA7 - 5527 - 75
12SERSERARGARG(chain 'A' and resid 7 through 484)AA62 - 25482 - 274
13HISHISARGARG(chain 'A' and resid 7 through 484)AA271 - 320291 - 340
14ASPASPHISHIS(chain 'A' and resid 7 through 484)AA330 - 484350 - 504
21GLNGLNGLUGLU(chain 'B' and (resid 7 through 55 or resid 62 through 254 or resid 271 through 484))BB7 - 5527 - 75
22SERSERARGARG(chain 'B' and (resid 7 through 55 or resid 62 through 254 or resid 271 through 484))BB62 - 25482 - 274
23HISHISARGARG(chain 'B' and (resid 7 through 55 or resid 62 through 254 or resid 271 through 484))BB271 - 320291 - 340
24ASPASPHISHIS(chain 'B' and (resid 7 through 55 or resid 62 through 254 or resid 271 through 484))BB330 - 484350 - 504

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycosyltransferase


Mass: 57629.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytolacca americana (American pokeweed)
Gene: PaGT3 / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B5MGN9, Transferases; Glycosyltransferases; Hexosyltransferases

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Non-polymers , 5 types, 169 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O6
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23FN2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.15-0.20 M potassium acetate 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→35.05 Å / Num. obs: 58912 / % possible obs: 99.55 % / Redundancy: 6.7 % / Biso Wilson estimate: 45.64 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 19.96
Reflection shellResolution: 2.15→2.22 Å / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 5680 / CC1/2: 0.81 / Rpim(I) all: 0.32 / Rrim(I) all: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6lzy

6lzy


Resolution: 2.15→35.05 Å / SU ML: 0.3356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8226
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.254 2977 5.05 %
Rwork0.2135 55931 -
obs0.2157 58908 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.58 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7199 0 95 164 7458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00457472
X-RAY DIFFRACTIONf_angle_d0.742910105
X-RAY DIFFRACTIONf_chiral_restr0.04811103
X-RAY DIFFRACTIONf_plane_restr0.00431271
X-RAY DIFFRACTIONf_dihedral_angle_d24.15672742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.32521380.28832459X-RAY DIFFRACTION93.92
2.19-2.230.34811410.28882631X-RAY DIFFRACTION99.96
2.23-2.270.33991620.28552634X-RAY DIFFRACTION100
2.27-2.310.33741460.28362636X-RAY DIFFRACTION99.89
2.31-2.360.31091080.2762654X-RAY DIFFRACTION99.93
2.36-2.410.32461370.26442655X-RAY DIFFRACTION99.96
2.41-2.460.32811500.26822629X-RAY DIFFRACTION99.78
2.46-2.530.30391460.26092649X-RAY DIFFRACTION99.96
2.53-2.590.35541240.26352666X-RAY DIFFRACTION99.96
2.59-2.670.3351300.2672650X-RAY DIFFRACTION100
2.67-2.760.35161390.25452673X-RAY DIFFRACTION100
2.76-2.850.32221280.25462666X-RAY DIFFRACTION99.96
2.85-2.970.32551130.26462705X-RAY DIFFRACTION99.93
2.97-3.10.2677980.25022681X-RAY DIFFRACTION99.96
3.1-3.270.30331610.2432677X-RAY DIFFRACTION100
3.27-3.470.29881470.23422671X-RAY DIFFRACTION99.96
3.47-3.740.23831460.2172685X-RAY DIFFRACTION99.93
3.74-4.110.24081790.18592660X-RAY DIFFRACTION99.79
4.12-4.710.21041740.16532678X-RAY DIFFRACTION99.41
4.71-5.930.21831360.17262734X-RAY DIFFRACTION99.48
5.93-35.050.17931740.16662838X-RAY DIFFRACTION99.5

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