[English] 日本語
Yorodumi
- PDB-7nc6: Glutathione-S-transferase GliG in complex with cyclo[L-Phe-L-Ser]... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nc6
TitleGlutathione-S-transferase GliG in complex with cyclo[L-Phe-L-Ser]-bis-glutathione-adduct
ComponentsGlutathione S-transferase GliG
KeywordsBIOSYNTHETIC PROTEIN / Aspergillus fumigatus / mycotoxin / glutathione-S-transferase / carbon-sulphur-bond / epidithiodioxopiperazine
Function / homology
Function and homology information


glutathione transferase / molecular function activator activity
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
ACETATE ION / Chem-U8B / glutathione transferase
Similarity search - Component
Biological speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGroll, M. / Huber, E.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural and Mechanistic Insights into C-S Bond Formation in Gliotoxin.
Authors: Scherlach, K. / Kuttenlochner, W. / Scharf, D.H. / Brakhage, A.A. / Hertweck, C. / Groll, M. / Huber, E.M.
History
DepositionJan 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,45316
Polymers173,7786
Non-polymers3,67510
Water4,864270
1
A: Glutathione S-transferase GliG
B: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2527
Polymers57,9262
Non-polymers1,3265
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-17 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: Glutathione S-transferase GliG
D: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1315
Polymers57,9262
Non-polymers1,2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-21 kcal/mol
Surface area19590 Å2
MethodPISA
3
E: Glutathione S-transferase GliG
F: Glutathione S-transferase GliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0694
Polymers57,9262
Non-polymers1,1432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-16 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.370, 85.300, 344.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Glutathione S-transferase GliG


Mass: 28963.014 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus A1163 (mold) / Gene: AFUB_075740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0Y813
#2: Chemical
ChemComp-U8B / (2~{S})-2-azanyl-5-[[(2~{R})-3-[(2~{R},5~{R})-5-(hydroxymethyl)-3,6-bis(oxidanylidene)-2-(phenylmethyl)-5-sulfanyl-piperazin-2-yl]sulfanyl-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid


Mass: 571.624 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H29N5O9S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M bis-tris pH 5.5, 25 % PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 92409 / % possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 11933

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NC3

7nc3


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 17 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 4619 5 %RANDOM
Rwork0.1832 ---
obs0.1859 87753 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.98 Å2 / Biso mean: 48.54 Å2 / Biso min: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å2-0 Å2-0 Å2
2--1.74 Å2-0 Å2
3---2.22 Å2
Refinement stepCycle: final / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11569 0 208 270 12047
Biso mean--70.29 51.44 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01312082
X-RAY DIFFRACTIONr_bond_other_d0.0030.01711299
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.6716406
X-RAY DIFFRACTIONr_angle_other_deg1.1961.59626185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92651422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04221.523637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.082152071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0191590
X-RAY DIFFRACTIONr_chiral_restr0.0510.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022607
X-RAY DIFFRACTIONr_rigid_bond_restr0.819323379
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 338 -
Rwork0.261 6416 -
all-6754 -
obs--99.82 %
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)
10.15520.0216-0.050.0205-0.03150.1047-0.00620.014-0.0025-0.0041-0.0062-0.00260.00610.00490.01240.13920.00090.00210.0570.00310.0136-16.089-5.64757.621
20.13120.0163-0.07290.0144-0.02790.1495-0.0043-0.0296-0.0010.0006-0.00920.0090.00590.0180.01360.1357-0.00120.00050.05880.00230.0172-17.203-4.62981.19
30.0420.03110.02480.1666-0.01980.1064-0.00370.0048-0.0002-0.00680.0011-0.01690.004-0.01120.00260.1335-0.00180.00450.055-0.0090.0181-14.38-4.364115.207
40.0332-0.0031-0.0130.0832-0.02680.1212-0.0039-0.00540.0030.01530.0033-0.0192-0.0077-0.00990.00070.1366-0.0007-0.00130.0558-0.00810.0163-14.1480.044138.389
50.03510.0433-0.02450.08670.02590.197-0.0036-0.0160.0032-0.0189-0.01760.0101-0.0214-0.01210.02120.14070.0085-0.00960.056-0.01550.0152-13.3651.706172.831
60.05870.0107-0.03240.1470.03410.22310.005-0.05830.0136-0.0015-0.02260.0115-0.02110.01270.01760.14160.001-0.00490.0757-0.01790.0066-10.1214.272196.095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 239
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B2 - 239
4X-RAY DIFFRACTION2B301
5X-RAY DIFFRACTION3C1 - 239
6X-RAY DIFFRACTION3C301
7X-RAY DIFFRACTION4D3 - 239
8X-RAY DIFFRACTION4D301
9X-RAY DIFFRACTION5E2 - 239
10X-RAY DIFFRACTION5E301
11X-RAY DIFFRACTION6F3 - 239
12X-RAY DIFFRACTION6F301

+
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