[English] 日本語
Yorodumi
- PDB-6pnt: Structural Characterization of UDP-glycosyltransferase from Tetra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pnt
TitleStructural Characterization of UDP-glycosyltransferase from Tetranychus Urticae
ComponentsUDP-glycosyltransferase 202A2
KeywordsTRANSFERASE / Uridine diphosphate / UDP-glycosyltransferase / Two-spotted Spider Mite / Pesticide detoxification
Function / homology: / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDaneshian, L. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
CitationJournal: To Be Published
Title: Structural Characterization of UDP-glycosyltransferase from Tetranychus Urticae
Authors: Daneshian, L. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
History
DepositionJul 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glycosyltransferase 202A2


Theoretical massNumber of molelcules
Total (without water)48,9511
Polymers48,9511
Non-polymers00
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.481, 77.481, 130.953
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein UDP-glycosyltransferase 202A2


Mass: 48950.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Gene: 107367435, UGT202A2 / Plasmid: pET100/D-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: T1KUK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 10% PEG 5000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 39554 / % possible obs: 99.3 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.032 / Rrim(I) all: 0.09 / Rsym value: 0.083 / Net I/σ(I): 33.32
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1947 / CC1/2: 0.731 / Rpim(I) all: 0.267 / Rrim(I) all: 0.684 / Rsym value: 0.627 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IYA

2iya


Resolution: 1.85→29.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1944 4.9 %RANDOM
Rwork0.1682 ---
obs0.1701 37336 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.23 Å2 / Biso mean: 31.231 Å2 / Biso min: 19.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.22 Å2-0 Å2
2---0.45 Å20 Å2
3---1.45 Å2
Refinement stepCycle: final / Resolution: 1.85→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 0 380 3737
Biso mean---41.22 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133436
X-RAY DIFFRACTIONr_bond_other_d0.0340.0173290
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.6364651
X-RAY DIFFRACTIONr_angle_other_deg2.3161.5737660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55323.038158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0215614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8091515
X-RAY DIFFRACTIONr_chiral_restr0.1420.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023778
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02675
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 154 -
Rwork0.246 2725 -
all-2879 -
obs--99.48 %
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)
11.6058-0.1116-0.21382.3438-0.63921.66820.08990.1205-0.0429-0.3809-0.08330.01490.0777-0.0848-0.00650.1967-0.0050.01180.1169-0.00240.0034-5.3132.868-10.086
20.5881-0.4287-0.191.47210.24010.2963-0.0247-0.0730.01370.0834-0.0021-0.0544-0.00320.02390.02670.1442-0.0271-0.00160.1226-0.00210.0076-9.62944.3424.116
31.27610.61280.30260.53430.26971.1149-0.0809-0.00930.0586-0.173-0.0080.1644-0.1038-0.07590.0890.1853-0.0086-0.08220.0931-0.01050.0808-29.96350.137-10.654
45.9786-4.32420.76096.0954-1.00990.24730.12510.1950.3463-0.6566-0.2142-0.5588-0.02690.07980.08910.332-0.0260.06980.14860.01460.0523-4.27854.925-13.258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 72
2X-RAY DIFFRACTION2A73 - 259
3X-RAY DIFFRACTION3A260 - 400
4X-RAY DIFFRACTION4A401 - 436

+
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