[English] 日本語
Yorodumi
- PDB-5o84: Glutathione S-transferase Tau 23 (partially oxidized) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o84
TitleGlutathione S-transferase Tau 23 (partially oxidized)
ComponentsGlutathione S-transferase U23
KeywordsTRANSFERASE / Glutathione S-transferase / Tau
Function / homology
Function and homology information


toxin catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like ...Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / 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 / 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
ACETATE ION / FORMIC ACID / Glutathione S-transferase U23
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsYoung, D.R. / Van Molle, I. / Tossounian, M. / Messens, J.
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Disulfide bond formation protects Arabidopsis thaliana glutathione transferase tau 23 from oxidative damage.
Authors: Tossounian, M.A. / Van Molle, I. / Wahni, K. / Jacques, S. / Gevaert, K. / Van Breusegem, F. / Vertommen, D. / Young, D. / Rosado, L.A. / Messens, J.
History
DepositionJun 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione S-transferase U23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8039
Polymers25,3361
Non-polymers4678
Water2,126118
1
A: Glutathione S-transferase U23
hetero molecules

A: Glutathione S-transferase U23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,60618
Polymers50,6722
Non-polymers93316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5770 Å2
ΔGint-7 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.165, 50.740, 57.167
Angle α, β, γ (deg.)90.000, 112.470, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Glutathione S-transferase U23 / AtGSTU23 / GST class-tau member 23


Mass: 25336.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSTU23, At1g78320, F3F9.14 / Plasmid: pDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q9M9F1, glutathione transferase

-
Non-polymers , 6 types, 126 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.16 M MgCl2, 0.08 M Tris-HCl pH 8.5, 24% PEG 4000, 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→42.64 Å / Num. obs: 19633 / % possible obs: 93.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.034 / Rrim(I) all: 0.063 / Net I/σ(I): 15.5 / Num. measured all: 65778 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8420.66812756430.6090.6030.9051.252.2
9.01-42.6430.0255051700.9990.0170.035291.9

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vo4

2vo4


Resolution: 1.88→30.26 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 870 4.8 %Random
Rwork0.1809 17246 --
obs0.1827 18116 97.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.35 Å2 / Biso mean: 31.3972 Å2 / Biso min: 7.92 Å2
Refinement stepCycle: final / Resolution: 1.88→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 62 118 1936
Biso mean--56.49 36.98 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091872
X-RAY DIFFRACTIONf_angle_d1.0152539
X-RAY DIFFRACTIONf_chiral_restr0.053272
X-RAY DIFFRACTIONf_plane_restr0.006320
X-RAY DIFFRACTIONf_dihedral_angle_d17.94699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8801-1.99790.27381300.25992609273990
1.9979-2.15210.22451460.196829213067100
2.1521-2.36860.22691270.189829573084100
2.3686-2.71110.22581480.1929123060100
2.7111-3.4150.20971720.184428923064100
3.415-30.2640.20481470.15852955310298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.09010.18945.72045.3103-1.97687.23410.15170.32471.34340.6839-0.2111-0.6508-1.9391.15780.14840.5643-0.18510.19360.53010.02750.53466.593230.939512.9794
23.21880.4953-0.15092.74221.0014.0114-0.07790.1924-0.1359-0.06570.0757-0.08010.16930.37180.00080.19530.00850.00330.23350.01870.1905-3.94418.837910.5437
37.25993.7018-3.08126.54640.94945.41420.07310.60190.068-0.45530.014-0.5668-0.38340.4314-0.07620.3971-0.04840.0220.27890.08760.2949-4.365632.97018.5531
48.0177-0.23381.39127.4070.21237.913-0.169-0.2614-0.89180.14380.3892-0.4410.64271.1012-0.21280.3270.01290.11130.53120.01930.40015.918916.81459.562
51.5831-2.2514-1.77314.71921.04566.55520.5795-0.192-0.63810.3194-0.042-0.00120.1844-0.1988-0.43480.40120.0507-0.00340.9624-0.04130.646810.285214.930718.1574
63.1312-0.0120.7085.83950.84215.278-0.57-1.1209-0.08850.13610.5322-0.53180.6660.2509-0.18280.65220.1707-0.00350.70940.02440.49724.809715.178923.9013
75.06290.54040.11372.14322.28974.7190.2628-0.15070.04520.1203-0.283-0.7723-0.030.5260.00540.1584-0.02840.00040.3460.02350.24342.603121.850917.3521
85.15053.8974-0.59823.1326-0.47712.79960.0166-0.7326-0.3512-0.0571-0.1165-0.7537-0.03120.81960.20070.2106-0.02170.00180.3711-0.02490.36432.568424.54821.4259
95.181-1.04480.81476.4272-0.50443.27140.10840.01490.5463-0.1352-0.0956-0.0089-0.59930.22120.04730.2829-0.04070.01690.18120.01120.2482-5.986331.714618.6966
101.7472-0.14491.41184.2827-1.24591.43910.0553-0.0410.51890.24370.14680.2426-0.5257-0.4835-0.2870.26450.0941-0.02910.15720.0170.236-17.975933.001920.6304
112.65270.90170.56923.06913.20985.420.05750.00980.02540.1253-0.19240.16640.0161-0.32550.09640.16060.0096-0.01980.14790.01730.1565-17.428321.411122.9063
126.29290.1796-1.64866.48522.60647.39180.1291-0.4239-1.48570.3416-0.0382-0.74941.42270.72720.09070.49060.118-0.03820.2970.0320.4758-12.51558.186719.3828
138.25411.4756-3.63646.2264-2.60587.6408-0.3593-0.029-1.03080.85260.182-0.23580.5354-0.23460.12410.67680.050.00490.40240.04540.4822-12.0291-1.054213.2209
146.7028-3.14441.78158.22614.03493.9875-0.6853-0.4935-0.82840.87180.49450.69281.2506-0.74720.32370.394-0.03340.02990.28680.02070.2685-21.0475.481815.0164
154.432-1.44570.33135.65710.86363.832-0.08620.0710.02030.10260.19880.69760.0013-0.7256-0.0220.1518-0.0067-0.00790.25980.01730.2299-26.608417.638913.7638
161.01880.72880.51871.2673-0.21971.21120.0540.27840.1338-0.2692-0.11330.0733-0.0684-0.2241-0.07540.16060.0317-0.02850.16350.0430.1458-18.478824.596311.424
175.31631.52270.38492.89181.0531.76760.01870.5139-0.2332-0.13680.0450.02510.402-0.0046-0.05720.33060.0071-0.0430.2917-0.0590.222-17.04617.56223.9212
185.74334.8625-1.0967.5828-1.75863.20440.04380.3346-0.0087-0.4603-0.07140.2109-0.0304-0.2579-0.01720.24570.0542-0.05760.25790.00430.2098-21.710520.17464.0116
192.3042-1.2229-0.39157.98452.87172.8895-0.05650.2982-0.2884-0.66570.3583-0.19970.16940.1054-0.28960.26030.00860.00750.3289-0.01910.229-7.046312.64651.2902
207.2802-1.2431-5.14590.56121.70295.6-1.4225-1.5305-2.90820.20230.12030.12991.84560.68041.16810.66480.05030.10640.50350.13160.6635-3.9911-4.47745.7609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:6)A2 - 6
2X-RAY DIFFRACTION2(chain A and resid 7:23)A7 - 23
3X-RAY DIFFRACTION3(chain A and resid 24:29)A24 - 29
4X-RAY DIFFRACTION4(chain A and resid 30:39)A30 - 39
5X-RAY DIFFRACTION5(chain A and resid 40:46)A40 - 46
6X-RAY DIFFRACTION6(chain A and resid 47:52)A47 - 52
7X-RAY DIFFRACTION7(chain A and resid 53:59)A53 - 59
8X-RAY DIFFRACTION8(chain A and resid 60:67)A60 - 67
9X-RAY DIFFRACTION9(chain A and resid 68:81)A68 - 81
10X-RAY DIFFRACTION10(chain A and resid 82:91)A82 - 91
11X-RAY DIFFRACTION11(chain A and resid 92:104)A92 - 104
12X-RAY DIFFRACTION12(chain A and resid 105:109)A105 - 109
13X-RAY DIFFRACTION13(chain A and resid 111:123)A111 - 123
14X-RAY DIFFRACTION14(chain A and resid 124:130)A124 - 130
15X-RAY DIFFRACTION15(chain A and resid 131:142)A131 - 142
16X-RAY DIFFRACTION16(chain A and resid 143:160)A143 - 160
17X-RAY DIFFRACTION17(chain A and resid 161:177)A161 - 177
18X-RAY DIFFRACTION18(chain A and resid 178:192)A178 - 192
19X-RAY DIFFRACTION19(chain A and resid 193:212)A193 - 212
20X-RAY DIFFRACTION20(chain A and resid 213:218)A213 - 218

+
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