[English] 日本語
Yorodumi
- PDB-7so8: Crystal structure of Glutathione S-Transferase from Shrimp Litope... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7so8
TitleCrystal structure of Glutathione S-Transferase from Shrimp Litopenaeus vannamei in complex with silver ions and a molecules of Glutathione binding in G-site and H-site
ComponentsGlutathione transferase
KeywordsTRANSFERASE / GST / GSH binding in G-site
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, Mu class / 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, Mu class / 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 / Thioredoxin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
SILVER ION / GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesPenaeus vannamei (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsEscudero-Garcia, A. / Rudino-Pinera, E. / Miranda-Blancas, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Inhibition of GST class Mu of the shrimp Litopenaeus vannamei by binding silver ions in H-site.
Authors: Escudero-Garcia, A. / Rudino-Pinera, E.
History
DepositionOct 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione transferase
C: Glutathione transferase
E: Glutathione transferase
G: Glutathione transferase
H: Glutathione transferase
F: Glutathione transferase
B: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,05522
Polymers204,4208
Non-polymers3,63514
Water20,9331162
1
A: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0275
Polymers51,1052
Non-polymers9223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-28 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0666
Polymers51,1052
Non-polymers9614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-30 kcal/mol
Surface area19240 Å2
MethodPISA
3
E: Glutathione transferase
hetero molecules

F: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1356
Polymers51,1052
Non-polymers1,0304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4420 Å2
ΔGint-39 kcal/mol
Surface area18810 Å2
MethodPISA
4
G: Glutathione transferase
H: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8275
Polymers51,1052
Non-polymers7233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-30 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.390, 93.020, 169.110
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glutathione transferase


Mass: 25552.455 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei (Pacific white shrimp)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q49SB0, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 6.5
Details: 100 mM ammonium sulphate, 100 Bis-Tris pH 6.5, 30% PEG 3350, 300 uM silver nitrate
PH range: 6.5-8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 12, 2019 / Details: Sagitally focusing 2nd Crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→56.37 Å / Num. obs: 88718 / % possible obs: 98.15 % / Redundancy: 3.104 % / Biso Wilson estimate: 13.76 Å2 / CC1/2: 0.627 / Rmerge(I) obs: 0.6179 / Rpim(I) all: 0.4226 / Rrim(I) all: 0.7511 / Net I/av σ(I): 1.98 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.370.5792.1175300.660.3960.70497.6
2.37-2.610.3973.1176630.8140.2710.48398
2.61-2.990.2664.5176410.9140.1820.32498.2
2.99-3.760.1228.7178490.9830.0840.14998.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSVERSION Jan 26,2018data reduction
XSCALEVERSION Jan 26, 2018data scaling
PHASER7.0.076phasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AN1

5an1


Resolution: 2.2→56.37 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 4472 5.04 %
Rwork0.1914 84236 -
obs0.1949 88708 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.29 Å2 / Biso mean: 16.3226 Å2 / Biso min: 1.6 Å2
Refinement stepCycle: final / Resolution: 2.2→56.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14400 0 219 1162 15781
Biso mean--41.67 18.6 -
Num. residues----1751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.220.31111410.23752792293397
2.22-2.250.3221470.22922727287498
2.25-2.280.29481550.23362832298798
2.28-2.310.29971660.22872754292098
2.31-2.340.31311330.22612748288197
2.34-2.370.31251300.22352815294598
2.37-2.40.30551370.22222797293498
2.4-2.440.31241600.22392762292298
2.44-2.480.28761290.21162847297698
2.48-2.520.28791200.21432789290998
2.52-2.560.31521600.21292747290798
2.56-2.610.29591410.20732890303198
2.61-2.660.25851480.21212732288098
2.66-2.710.2911630.21132776293998
2.71-2.770.27691520.20652784293698
2.77-2.840.31591400.21352851299198
2.84-2.910.30081520.21462794294698
2.91-2.990.29311550.20622800295598
2.99-3.070.30481400.20922820296099
3.07-3.170.29841620.19652829299199
3.17-3.290.24921780.20742762294099
3.29-3.420.29521550.19032856301199
3.42-3.570.23071290.16972857298699
3.57-3.760.23261470.15962816296399
3.76-40.21681720.15362795296799
4-4.310.21131570.13742837299499
4.31-4.740.18221440.13442876302099
4.74-5.420.20211710.14712811298298
5.42-6.830.18961270.18172875300298
6.83-56.370.18581610.18512865302697

+
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