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- PDB-6jem: Structure of Phytolacca americana UGT2 complexed with UDP-2fluoro... -

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Basic information

Entry
Database: PDB / ID: 6jem
TitleStructure of Phytolacca americana UGT2 complexed with UDP-2fluoro-glucose and resveratrol
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase 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
RESVERATROL / Chem-U2F / Glycosyltransferase
Similarity search - Component
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMaharjan, R. / Fukuda, Y. / Nakayama, T. / Hamada, H. / Ozaki, S. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
CitationJournal: Biochemistry / Year: 2020
Title: An Ambidextrous Polyphenol GlycosyltransferasePaGT2 fromPhytolacca americana.
Authors: Maharjan, R. / Fukuda, Y. / Shimomura, N. / Nakayama, T. / Okimoto, Y. / Kawakami, K. / Nakayama, T. / Hamada, H. / Inoue, T. / Ozaki, S.I.
History
DepositionFeb 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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: Glycosyltransferase
B: Glycosyltransferase
C: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,8779
Polymers161,4883
Non-polymers2,3906
Water00
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6263
Polymers53,8291
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-3 kcal/mol
Surface area19330 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6263
Polymers53,8291
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-2 kcal/mol
Surface area19030 Å2
MethodPISA
3
C: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6263
Polymers53,8291
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-2 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.374, 137.616, 208.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA5 - 46625 - 486
21GLNGLNBB5 - 46625 - 486
12TRPTRPAA5 - 46425 - 484
22TRPTRPCC5 - 46425 - 484
13LYSLYSBB5 - 46325 - 483
23LYSLYSCC5 - 46325 - 483

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Glycosyltransferase


Mass: 53829.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytolacca americana (American pokeweed)
Gene: PaGT2 / Plasmid: pCold / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): star
References: UniProt: B5MGN7, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#3: Chemical ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H12O3
Has ligand of interestN
Sequence detailsThe sequence database with ID B5MGN7 contains residue TYR at position 211. However, after observing ...The sequence database with ID B5MGN7 contains residue TYR at position 211. However, after observing the discrepancy, authors confirmed that residue at 211 is ASN and not TYR. The depositers will soon correct the sequence in the database.

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.11 M potassium citrate 0.06 M lithium citrate 0.11 M sodium phosphate 23% w/v PEG 6000

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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: RAYONIX MX300HE / Detector: CCD / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 51665 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.04 / Net I/σ(I): 25.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2535 / CC1/2: 0.689 / Rrim(I) all: 0.514 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VCH

2vch


Resolution: 2.6→44.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.578 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25225 2598 5 %RANDOM
Rwork0.1927 ---
obs0.19573 48996 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.087 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.6→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10087 0 159 0 10246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310499
X-RAY DIFFRACTIONr_bond_other_d0.0350.0179840
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.64414330
X-RAY DIFFRACTIONr_angle_other_deg2.321.56922858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11751299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5222.376463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.754151683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3471553
X-RAY DIFFRACTIONr_chiral_restr0.0750.21375
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211485
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022082
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.687.7575226
X-RAY DIFFRACTIONr_mcbond_other7.6797.7575225
X-RAY DIFFRACTIONr_mcangle_it10.74211.6426515
X-RAY DIFFRACTIONr_mcangle_other10.74211.6426516
X-RAY DIFFRACTIONr_scbond_it7.9088.4355273
X-RAY DIFFRACTIONr_scbond_other7.9088.4375274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.4312.3577816
X-RAY DIFFRACTIONr_long_range_B_refined14.48191.15711020
X-RAY DIFFRACTIONr_long_range_B_other14.48191.15911021
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A128200.11
12B128200.11
21A127020.12
22C127020.12
31B126390.12
32C126390.12
LS refinement shellResolution: 2.595→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 188 -
Rwork0.312 3512 -
obs--98.46 %

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