[English] 日本語
Yorodumi
- PDB-3ein: Delta class GST -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ein
TitleDelta class GST
ComponentsGlutathione S-transferase 1-1
KeywordsTRANSFERASE / glutathione S-transferase / glutathione / delta-class GST
Function / homology
Function and homology information


DDT-dehydrochlorinase / DDT-dehydrochlorinase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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 D1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.126 Å
AuthorsFeil, S.C.
CitationJournal: To be Published
Title: Probing insect detoxification systems
Authors: Feil, S.C. / Low, W.Y. / Ng, H.L. / Pyke, J. / Gooley, P. / Parker, M.W. / Robin, C. / McConville, M. / Batterham, P.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2011Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2002
Polymers23,8921
Non-polymers3071
Water4,648258
1
A: Glutathione S-transferase 1-1
hetero molecules

A: Glutathione S-transferase 1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3994
Polymers47,7852
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3980 Å2
ΔGint-33.2 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.775, 63.212, 54.513
Angle α, β, γ (deg.)90.000, 129.840, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Glutathione S-transferase 1-1 / GST class-theta


Mass: 23892.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GstD1, GST, Gst1, CG10045 / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20432, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25%(w/v) PEG3350, 0.2M NaCl, 100mM HEPES, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2007 / Details: mirrors
RadiationMonochromator: bent conical Si mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Av σ(I) over netI: 26 / Number: 280016 / Rmerge(I) obs: 0.048 / Χ2: 1.39 / D res high: 1.13 Å / D res low: 50 Å / Num. obs: 69523 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.435099.110.040.9585.9
1.932.4310010.0541.3896.4
1.691.9399.810.0541.4373.6
1.531.6910010.0581.3693.7
1.421.5399.910.0711.4953.6
1.341.4299.910.0861.4833.6
1.271.3499.910.1011.4943.6
1.221.2799.710.1291.5963.5
1.171.2299.510.1591.5373.4
1.131.179410.1961.6093
ReflectionResolution: 1.13→50 Å / Num. obs: 69523 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.048 / Χ2: 1.389
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 3 % / Rmerge(I) obs: 0.196 / Num. unique all: 6602 / Χ2: 1.609 / % possible all: 94

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.126→31.61 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.92 / SU B: 0.803 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.157 3504 5 %RANDOM
Rwork0.14 ---
obs0.141 66014 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.1 Å2 / Biso mean: 13.938 Å2 / Biso min: 5.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.03 Å2
2---0.35 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.126→31.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 20 258 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221823
X-RAY DIFFRACTIONr_bond_other_d0.0080.021253
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9632490
X-RAY DIFFRACTIONr_angle_other_deg0.9533068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80324.23585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24215307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.539157
X-RAY DIFFRACTIONr_chiral_restr0.2480.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.2160.2419
X-RAY DIFFRACTIONr_nbd_other0.1710.21282
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2920
X-RAY DIFFRACTIONr_nbtor_other0.0850.2838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.229
X-RAY DIFFRACTIONr_mcbond_it2.2721419
X-RAY DIFFRACTIONr_mcbond_other1.5192426
X-RAY DIFFRACTIONr_mcangle_it2.62731751
X-RAY DIFFRACTIONr_scbond_it2.7022921
X-RAY DIFFRACTIONr_scangle_it3.43727
X-RAY DIFFRACTIONr_rigid_bond_restr1.54633966
X-RAY DIFFRACTIONr_sphericity_free10.2383264
X-RAY DIFFRACTIONr_sphericity_bonded6.54733015
LS refinement shellResolution: 1.126→1.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 219 -
Rwork0.244 4131 -
all-4350 -
obs--83.59 %

+
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