[English] 日本語
Yorodumi
- PDB-6b51: Schistosoma haematobium (Blood Fluke) Sulfotransferase, Y54F Mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b51
TitleSchistosoma haematobium (Blood Fluke) Sulfotransferase, Y54F Mutant
ComponentsSulfotransferase
KeywordsTRANSFERASE / sulfotransferase / parasite / helminth
Function / homology
Function and homology information


Sulfotransferase, S. mansonii-type / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Nad dependent epimerase/dehydratase
Similarity search - Component
Biological speciesSchistosoma haematobium (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTaylor, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI115691 United States
CitationJournal: Int.J.Parasitol. / Year: 2020
Title: Why does oxamniquine kill Schistosoma mansoni and not S. haematobium and S. japonicum?
Authors: Rugel, A.R. / Guzman, M.A. / Taylor, A.B. / Chevalier, F.D. / Tarpley, R.S. / McHardy, S.F. / Cao, X. / Holloway, S.P. / Anderson, T.J.C. / Hart, P.J. / LoVerde, P.T.
History
DepositionSep 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3Oct 4, 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: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7963
Polymers29,2471
Non-polymers5492
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-2 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.861, 71.957, 139.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

-
Components

#1: Protein Sulfotransferase


Mass: 29246.564 Da / Num. of mol.: 1 / Mutation: Y54F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma haematobium (invertebrata) / Gene: MS3_07706 / Plasmid: pAG8H / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 pLysS
References: UniProt: A0A094ZWQ2, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.06 M (magnesium chloride, calcium chloride), 0.1 M (Tris, Bicine), pH 8.5, 37.5% (MPD, PEG1000, PEG3350)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→139.32 Å / Num. obs: 16155 / % possible obs: 96.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 39.4 Å2 / Rpim(I) all: 0.032 / Rsym value: 0.069 / Net I/σ(I): 13.3
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2202 / Rpim(I) all: 0.336 / Rsym value: 0.708 / % possible all: 92

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TIV

5tiv


Resolution: 2.05→69.659 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.89
RfactorNum. reflection% reflection
Rfree0.2428 1608 10 %
Rwork0.1982 --
obs0.2029 16087 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 2.05→69.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 35 48 2093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012093
X-RAY DIFFRACTIONf_angle_d1.312840
X-RAY DIFFRACTIONf_dihedral_angle_d13.581790
X-RAY DIFFRACTIONf_chiral_restr0.054314
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11620.32951350.32791216X-RAY DIFFRACTION89
2.1162-2.19180.33321360.25351227X-RAY DIFFRACTION93
2.1918-2.27960.34871390.24521245X-RAY DIFFRACTION92
2.2796-2.38340.31641410.25381265X-RAY DIFFRACTION93
2.3834-2.5090.34181400.24781279X-RAY DIFFRACTION95
2.509-2.66620.29131480.23711333X-RAY DIFFRACTION98
2.6662-2.87210.31061500.24281349X-RAY DIFFRACTION99
2.8721-3.16110.27361540.2311376X-RAY DIFFRACTION100
3.1611-3.61850.23331480.20631343X-RAY DIFFRACTION98
3.6185-4.55880.20191550.15511392X-RAY DIFFRACTION100
4.5588-69.69870.1911620.1621454X-RAY DIFFRACTION99

+
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