[English] 日本語
Yorodumi
- PDB-7vel: Crystal structure of Phytolacca americana UGT3 with UDP-2fluoroglucose -

+
Open data


ID or keywords:

Loading...

-
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-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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 169 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / 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 / 18-Crown-6


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 / Water


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more