[English] 日本語
Yorodumi
- PDB-1oe7: 28kDa glutathione S-transferase from Schistosoma haematobium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oe7
Title28kDa glutathione S-transferase from Schistosoma haematobium
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / SCHISTOSOMIASIS / DETOXIFYING ENZYME / PROSTAGLANDIN D2 SYNTHASE / VACCINE CANDIDATE
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase class-mu 28 kDa isozyme
Similarity search - Component
Biological speciesSCHISTOSOMA HAEMATOBIUM (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJohnson, K.A. / Angelucci, F. / Tsernoglou, D.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal Structure of the 28 kDa Glutathione S-Transferase from Schistosoma Haematobium
Authors: Johnson, K.A. / Angelucci, F. / Bellelli, A. / Herve, M. / Fontaine, J. / Tsernoglou, D. / Capron, A. / Trottein, F. / Brunori, M.
#1: Journal: J.Exp.Med. / Year: 2001
Title: Role of the Parasite-Derived Prostaglandin D2 in the Inhibition of Epidermal Langerhans Cell Migration During Schistosomiasis Infections
Authors: Angeli, V. / Faveeuw, C. / Roye, O. / Fontaine, J. / Teissier, E. / Capron, A. / Wolowczuk, L. / Capron, M. / Trottein, F.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary Diffraction Studies of a Protective Cloned 28 kDa Glutathione S-Transferase from Schistosoma Mansoni
Authors: Trottein, F. / Vaney, M.C. / Bachet, B. / Pierce, R.J. / Colloc'H, N. / Lecocq, J.P. / Capron, A. / Momon, J.P.
History
DepositionMar 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4884
Polymers47,8732
Non-polymers6152
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.427, 78.111, 53.502
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0737, -0.0003, 0.9973), (-0.0011, -1, -0.0004), (0.9973, -0.0011, 0.0737)
Vector: -0.013, -20.023, 0.024)

-
Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 23936.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA HAEMATOBIUM (invertebrata) / Plasmid: PET-24D(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30114*PLUS, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE MAPPED AGAINST ITSELF PENDING SEQUENCE SUBMISSION TO SWISSPROT DATABASE FOR SCHISTOSOMA ...SEQUENCE MAPPED AGAINST ITSELF PENDING SEQUENCE SUBMISSION TO SWISSPROT DATABASE FOR SCHISTOSOMA HAEMATOBIUM SPECIES FOR THIS ENTRY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: PROTEIN (~60MG/ML) WAS CRYSTALLIZED IN HANGING DROPS USING A WELL SOLUTION OF 2.1M AMMONIUM SULFATE, 100MM TRIS, PH7.2, 5MM BETA-MERCAPTOETHANOL, pH 8.00
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.1 Mammonium sulfate1reservoir
2100 mMTris1reservoirpH7.2
35 mMbeta-mercaptoethanol1reservoir
466 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0032
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0032 Å / Relative weight: 1
ReflectionResolution: 1.81→25 Å / Num. obs: 39246 / % possible obs: 96.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 21.5
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.4 / % possible all: 72
Reflection
*PLUS
Redundancy: 6.5 % / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 72 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.4

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GTB

1gtb


Resolution: 1.8→20 Å / SU B: 3.62 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1958 5 %RANDOM
Rwork0.229 ---
obs-39158 96 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 40 225 3519
Refinement
*PLUS
Num. reflection obs: 39246 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.024
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.6

+
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