[English] 日本語
Yorodumi
- PDB-2vct: Glutathione transferase A2-2 in complex with delta-4-andostrene-3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vct
TitleGlutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione
ComponentsGLUTATHIONE S-TRANSFERASE A2
KeywordsTRANSFERASE / ANDOSTRENE DIONE / STEROID METABOLISM / GLUTATHIONE
Function / homology
Function and homology information


Glutathione conjugation / Azathioprine ADME / glutathione transferase / glutathione transferase activity / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / : / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, alpha class / : / 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 / 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
4-ANDROSTENE-3-17-DIONE / Glutathione S-transferase A2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTars, K. / Olin, B. / Mannervik, B.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Basis for Featuring of Steroid Isomerase Activity in Alpha Class Glutathione Transferases.
Authors: Tars, K. / Olin, B. / Mannervik, B.
History
DepositionSep 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: 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 1.4Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 A2
B: GLUTATHIONE S-TRANSFERASE A2
C: GLUTATHIONE S-TRANSFERASE A2
D: GLUTATHIONE S-TRANSFERASE A2
E: GLUTATHIONE S-TRANSFERASE A2
F: GLUTATHIONE S-TRANSFERASE A2
G: GLUTATHIONE S-TRANSFERASE A2
H: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,86612
Polymers205,7208
Non-polymers1,1464
Water29,2741625
1
A: GLUTATHIONE S-TRANSFERASE A2
B: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0034
Polymers51,4302
Non-polymers5732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-24 kcal/mol
Surface area20920 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE A2
D: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0034
Polymers51,4302
Non-polymers5732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-24.6 kcal/mol
Surface area21110 Å2
MethodPISA
3
E: GLUTATHIONE S-TRANSFERASE A2
F: GLUTATHIONE S-TRANSFERASE A2


Theoretical massNumber of molelcules
Total (without water)51,4302
Polymers51,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-23 kcal/mol
Surface area21050 Å2
MethodPISA
4
G: GLUTATHIONE S-TRANSFERASE A2
H: GLUTATHIONE S-TRANSFERASE A2


Theoretical massNumber of molelcules
Total (without water)51,4302
Polymers51,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-23.5 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.546, 97.343, 110.302
Angle α, β, γ (deg.)90.00, 115.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.14943, 0.76184, -0.63029), (0.74483, -0.50598, -0.43499), (-0.65031, -0.40445, -0.64305)39.841, -70.56317, -11.58124
2given(0.48901, -0.00317, -0.87227), (0.00073, -0.99999, 0.00404), (-0.87228, -0.00261, -0.48901)29.55214, -46.24124, 50.09357
3given(0.62526, -0.7608, 0.17387), (0.73873, 0.50515, -0.44621), (0.25165, 0.40744, 0.87787)58.77888, 24.29273, 20.52604
4given(-0.00988, 0.85131, -0.52458), (0.83664, -0.28028, -0.47062), (-0.54767, -0.44353, -0.70946)89.4124, -35.63917, -25.73468
5given(0.98541, 0.16923, -0.01835), (-0.16701, 0.98202, 0.08798), (0.03291, -0.08363, 0.99595)37.17848, 23.80718, -7.79124
6given(0.48875, -0.21038, -0.84668), (-0.20382, -0.97117, 0.12365), (-0.84828, 0.11214, -0.51754)21.91974, -21.23728, -32.58512
7given(0.42505, -0.86132, 0.27831), (0.82839, 0.24623, -0.50313), (0.36482, 0.44441, 0.81817)65.44708, 36.18267, -70.39578

-
Components

#1: Protein
GLUTATHIONE S-TRANSFERASE A2 / GLUTATHIONE-S-TRANSFERASE A2-2 / GTH2 / HA SUBUNIT 2 / GST-GAMMA / GSTA2-2 / GST CLASS-ALPHA MEMBER 2


Mass: 25715.006 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL BLUE / References: UniProt: P09210, glutathione transferase
#2: Chemical
ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE


Mass: 286.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1625 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsS112T IS A NATURAL VARIANT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.56 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: HANGING DROP VAPOUR TECHNIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN ...Details: HANGING DROP VAPOUR TECHNIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1UL OF 20 MM ANDROSTENE DIONE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2006 / Details: MIRRORS
RadiationMonochromator: DOUBLE SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 111829 / % possible obs: 99.8 % / Observed criterion σ(I): 1.6 / Redundancy: 3.6 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VCR

2vcr
PDB Unreleased entry


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.87 / SU B: 6.939 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 5956 5.1 %RANDOM
Rwork0.217 ---
obs0.221 111829 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-2.28 Å2
2---1.44 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14400 0 84 1625 16109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02214776
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4322.01119892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6851760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34224.39656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.434152920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0951588
X-RAY DIFFRACTIONr_chiral_restr0.0940.22188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.27616
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.210100
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.21416
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.2109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6641.59268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.095214288
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63536348
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.424.55604
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 450
Rwork0.246 8167

+
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