[English] 日本語
Yorodumi
- PDB-6mfe: Schistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0000773 (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mfe
TitleSchistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0000773 (Compound 11g) Complex
ComponentsSulfotransferase oxamniquine resistance protein
KeywordsTRANSFERASE / sulfotransferase / parasite / drug resistance
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 / Chem-S73 / Sulfotransferase oxamniquine resistance protein
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.444 Å
AuthorsTaylor, A.B.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Design, Synthesis, and Characterization of Novel Small Molecules as Broad Range Antischistosomal Agents.
Authors: Rugel, A. / Tarpley, R.S. / Lopez, A. / Menard, T. / Guzman, M.A. / Taylor, A.B. / Cao, X. / Kovalskyy, D. / Chevalier, F.D. / Anderson, T.J.C. / Hart, P.J. / LoVerde, P.T. / McHardy, S.F.
History
DepositionSep 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfotransferase oxamniquine resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9193
Polymers30,0811
Non-polymers8392
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-6 kcal/mol
Surface area12910 Å2
Unit cell
Length a, b, c (Å)140.553, 39.565, 53.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

-
Components

#1: Protein Sulfotransferase oxamniquine resistance protein


Mass: 30080.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: SULT-OR, Smp_089320 / Plasmid: pAG8H / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 pLysS / References: UniProt: G4VLE5
#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-S73 / (2-nitro-4-{[(3S)-1-{[4-(trifluoromethoxy)phenyl]methyl}pyrrolidin-3-yl]amino}phenyl)methanol


Mass: 411.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20F3N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0 M sodium citrate, 0.1 M sodium cacodylate, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.44→42.66 Å / Num. obs: 52276 / % possible obs: 95.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.1 Å2 / Rpim(I) all: 0.027 / Rsym value: 0.067 / Net I/σ(I): 17.2
Reflection shellResolution: 1.44→1.52 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6778 / Rpim(I) all: 0.351 / Rsym value: 0.818 / % possible all: 86.2

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MUA

4mua


Resolution: 1.444→42.656 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.28
RfactorNum. reflection% reflection
Rfree0.2105 2000 3.83 %
Rwork0.1648 --
obs0.1665 52225 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.444→42.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 56 339 2506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012221
X-RAY DIFFRACTIONf_angle_d1.3533024
X-RAY DIFFRACTIONf_dihedral_angle_d15.723835
X-RAY DIFFRACTIONf_chiral_restr0.072341
X-RAY DIFFRACTIONf_plane_restr0.006373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4443-1.48040.28721160.24042923X-RAY DIFFRACTION79
1.4804-1.52040.31161380.2243443X-RAY DIFFRACTION93
1.5204-1.56520.28971380.20443467X-RAY DIFFRACTION95
1.5652-1.61570.2411390.19583502X-RAY DIFFRACTION94
1.6157-1.67350.26621400.18273531X-RAY DIFFRACTION95
1.6735-1.74050.25681430.18013558X-RAY DIFFRACTION96
1.7405-1.81970.25351420.17543576X-RAY DIFFRACTION96
1.8197-1.91560.2341440.16873638X-RAY DIFFRACTION97
1.9156-2.03560.22391450.16883646X-RAY DIFFRACTION98
2.0356-2.19280.2161460.15223648X-RAY DIFFRACTION97
2.1928-2.41340.21231480.15473707X-RAY DIFFRACTION99
2.4134-2.76260.18241500.16193766X-RAY DIFFRACTION99
2.7626-3.48040.19241510.15933812X-RAY DIFFRACTION99
3.4804-42.67450.17931600.15124008X-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