[English] 日本語
Yorodumi
- PDB-2vcv: Glutathione transferase A3-3 in complex with glutathione and delt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vcv
TitleGlutathione transferase A3-3 in complex with glutathione and delta-4- androstene-3-17-dione
ComponentsGLUTATHIONE S-TRANSFERASE A3
KeywordsTRANSFERASE / ANDOSTRENE DIONE / STEROID METABOLISM / GLUTATHIONE
Function / homology
Function and homology information


Glutathione conjugation / NFE2L2 regulating anti-oxidant/detoxification enzymes / glutathione transferase / glutathione transferase activity / glutathione metabolic process / xenobiotic metabolic process / lipid metabolic process / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / : / 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 ...Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / : / 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 / Glutathione S-transferase A3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Feb 29, 2012Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.2May 29, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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 A3
B: GLUTATHIONE S-TRANSFERASE A3
C: GLUTATHIONE S-TRANSFERASE A3
D: GLUTATHIONE S-TRANSFERASE A3
E: GLUTATHIONE S-TRANSFERASE A3
F: GLUTATHIONE S-TRANSFERASE A3
G: GLUTATHIONE S-TRANSFERASE A3
H: GLUTATHIONE S-TRANSFERASE A3
I: GLUTATHIONE S-TRANSFERASE A3
J: GLUTATHIONE S-TRANSFERASE A3
K: GLUTATHIONE S-TRANSFERASE A3
L: GLUTATHIONE S-TRANSFERASE A3
M: GLUTATHIONE S-TRANSFERASE A3
N: GLUTATHIONE S-TRANSFERASE A3
O: GLUTATHIONE S-TRANSFERASE A3
P: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,48743
Polymers405,41916
Non-polymers8,06827
Water58,7833263
1
A: GLUTATHIONE S-TRANSFERASE A3
B: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,6772
Non-polymers1,1874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-24.1 kcal/mol
Surface area19420 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE A3
D: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5785
Polymers50,6772
Non-polymers9013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-25.8 kcal/mol
Surface area19910 Å2
MethodPISA
3
E: GLUTATHIONE S-TRANSFERASE A3
F: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,6772
Non-polymers1,1874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-23.1 kcal/mol
Surface area19440 Å2
MethodPISA
4
G: GLUTATHIONE S-TRANSFERASE A3
H: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,6772
Non-polymers1,1874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-23.3 kcal/mol
Surface area19420 Å2
MethodPISA
5
I: GLUTATHIONE S-TRANSFERASE A3
J: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5785
Polymers50,6772
Non-polymers9013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-25.7 kcal/mol
Surface area19840 Å2
MethodPISA
6
K: GLUTATHIONE S-TRANSFERASE A3
L: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,6772
Non-polymers1,1874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-21.5 kcal/mol
Surface area19490 Å2
MethodPISA
7
M: GLUTATHIONE S-TRANSFERASE A3
N: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2924
Polymers50,6772
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-28 kcal/mol
Surface area19970 Å2
MethodPISA
8
O: GLUTATHIONE S-TRANSFERASE A3
P: GLUTATHIONE S-TRANSFERASE A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5785
Polymers50,6772
Non-polymers9013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-24 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.177, 92.064, 113.540
Angle α, β, γ (deg.)89.76, 89.72, 89.73
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.92867, -0.37048, 0.01777), (-0.37086, 0.92824, -0.02884), (-0.00581, -0.03338, -0.99943)-78.02039, -14.43444, 31.83014
2given(0.94187, 0.3358, -0.01094), (0.33481, -0.9408, -0.05282), (-0.02803, 0.04609, -0.99854)36.48712, 30.46697, -40.72421
3given(-0.99927, 0.02157, 0.0314), (-0.02162, -0.99977, -0.00127), (0.03136, -0.00195, 0.99951)-43.46747, 18.55348, -70.37141
4given(0.93782, 0.3471, -0.0041), (0.34674, -0.93726, -0.03622), (-0.01641, 0.03255, -0.99934)-8.91992, 53.28581, -25.8986
5given(-0.99968, 0.01892, 0.01696), (-0.01884, -0.99981, 0.00455), (0.01705, 0.00423, 0.99985)-87.98461, 40.46713, -56.18718
6given(-0.99985, -0.01692, 0.0024), (-0.01693, 0.99985, -0.00407), (-0.00233, -0.00411, -0.99999)-42.07909, 23.59326, 101.84177
7given(0.93799, -0.34632, -0.01525), (0.34664, 0.93748, 0.03118), (0.0035, -0.03453, 0.9994)36.6148, 10.75115, 69.94672
8given(-0.99957, -0.01326, -0.02627), (-0.0133, 0.99991, 0.00145), (0.02625, 0.0018, -0.99965)-87.33016, 45.83342, 115.52911
9given(0.94069, -0.33926, 0.00287), (0.33856, 0.93924, 0.05658), (-0.02189, -0.05225, 0.99839)-7.31129, 33.4113, 85.1701
10given(1, -0.00128, -0.00257), (-0.00128, -1, -0.00085), (-0.00257, 0.00086, -1)45.33779, 63.94464, 44.79539
11given(-0.92799, 0.3723, -0.01517), (-0.3726, -0.92747, 0.03114), (-0.00248, 0.03455, 0.9994)-32.69117, 78.46609, 13.1007
12given(0.99936, 0.01139, -0.03395), (0.01174, -0.99988, 0.01011), (-0.03383, -0.0105, -0.99937)0.35277, 86.66576, 58.38307
13given(-0.93846, 0.34516, 0.01287), (-0.34397, -0.9373, 0.05614), (0.03144, 0.04826, 0.99834)-79.57493, 99.25872, 29.11652
14given(0.99967, -0.02, 0.01638), (0.02014, 0.99976, -0.0087), (-0.0162, 0.00902, 0.99983)44.55635, -23.03085, -14.29279
15given(-0.94035, -0.34022, 0.00033), (-0.33983, 0.93921, -0.04906), (0.01638, -0.04624, -0.9988)-34.93417, -35.06587, 16.24539

-
Components

#1: Protein
GLUTATHIONE S-TRANSFERASE A3 / GLUTATHIONE-S-TRANSFERASE A3-3 / GST CLASS-ALPHA MEMBER 3


Mass: 25338.678 Da / Num. of mol.: 16
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: Q16772, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE


Mass: 286.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C19H26O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3263 / 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: 2.09 Å3/Da / Density % sol: 40.79 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: HANGING VAPOUR DROP TECHIQUE 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 VAPOUR DROP TECHIQUE 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 25 MM ANDROSTENE DIONE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2006 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: THIN DIAMOND CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 338219 / % possible obs: 94.9 % / Observed criterion σ(I): 1.9 / Redundancy: 1.9 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TDI

1tdi


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.047 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 16208 5 %RANDOM
Rwork0.223 ---
obs0.225 304874 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å2-0.03 Å2-0.08 Å2
2---1.13 Å20.23 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28208 0 551 3263 32022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02229471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3312.02739679
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.253488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48623.8451251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.642155720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.97615209
X-RAY DIFFRACTIONr_chiral_restr0.0840.24383
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221601
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.215904
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.220049
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.23001
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.2155
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5031.518277
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.835228314
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.308312675
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0084.511353
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 1179
Rwork0.303 21923

+
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