[English] 日本語
Yorodumi
- PDB-8plp: Thioredoxin glutathione reductase of Schistosoma mansoni fragment... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8plp
TitleThioredoxin glutathione reductase of Schistosoma mansoni fragment screen hit 26.
ComponentsThioredoxin glutathione reductase
KeywordsFLAVOPROTEIN / Bi-functional / Oxidoreductase / Homodimer
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / (3R)-1-methylpiperidin-3-yl furan-2-carboxylate / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsRibeiro, L. / Montoya, B.O. / Moreira-Filho, J.T. / Bowyer, S. / Verma, A. / Neves, B.J. / Owens, R.J. / Andrade, C.H. / Silva-Jr, F.P. / Furnham, N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M026221/1 United Kingdom
Other government
Medical Research Council (MRC, United Kingdom)MR/K018779/1 United Kingdom
CitationJournal: Sci Rep / Year: 2024
Title: Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni.
Authors: de Souza Neto, L.R. / Montoya, B.O. / Brandao-Neto, J. / Verma, A. / Bowyer, S. / Moreira-Filho, J.T. / Dantas, R.F. / Neves, B.J. / Andrade, C.H. / von Delft, F. / Owens, R.J. / Furnham, N. / Silva-Jr, F.P.
History
DepositionJun 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin glutathione reductase
B: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,8376
Polymers129,8482
Non-polymers1,9904
Water16,250902
1
A: Thioredoxin glutathione reductase
hetero molecules

B: Thioredoxin glutathione reductase
hetero molecules


  • defined by author&software
  • Evidence: homology, REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 10430 ANGSTROM**2 ...Evidence: homology, REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 10430 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 47630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 1.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -0.50000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 1.00000
  • 132 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)131,8376
Polymers129,8482
Non-polymers1,9904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area10070 Å2
ΔGint-78 kcal/mol
Surface area47300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.103, 104.095, 134.786
Angle α, β, γ (deg.)90.000, 91.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Thioredoxin glutathione reductase


Mass: 64923.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: TGR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q962Y6, EC: 1.6.4.5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-WO1 / (3R)-1-methylpiperidin-3-yl furan-2-carboxylate


Mass: 209.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Calcium chloride dihydrate, 0.1 M Magnesium chloride hexahydrate, 0.1 M PIPES pH 7.0 and 22.5 % v/v PEG Smear Medium

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.28→29.64 Å / Num. obs: 77296 / % possible obs: 98.55 % / Redundancy: 1.9 % / Biso Wilson estimate: 39.04 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.29
Reflection shellResolution: 2.28→2.362 Å / Num. unique obs: 7314 / CC1/2: 0.681

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→29.64 Å / SU ML: 0.3213 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.8569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2298 3831 4.97 %
Rwork0.1885 73256 -
obs0.1907 77087 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.22 Å2
Refinement stepCycle: LAST / Resolution: 2.28→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9006 0 136 902 10044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089328
X-RAY DIFFRACTIONf_angle_d0.878912656
X-RAY DIFFRACTIONf_chiral_restr0.05341444
X-RAY DIFFRACTIONf_plane_restr0.00771608
X-RAY DIFFRACTIONf_dihedral_angle_d9.79011290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.310.41981080.37172250X-RAY DIFFRACTION80.53
2.31-2.340.33551420.29042681X-RAY DIFFRACTION98.95
2.34-2.370.30521520.27672704X-RAY DIFFRACTION98.21
2.37-2.40.28931210.2652699X-RAY DIFFRACTION98.19
2.4-2.440.35051290.2652693X-RAY DIFFRACTION98.84
2.44-2.480.29161140.2652766X-RAY DIFFRACTION98.26
2.48-2.520.33111320.26582708X-RAY DIFFRACTION99.13
2.52-2.560.29741390.25882694X-RAY DIFFRACTION98.47
2.56-2.610.32571630.26062717X-RAY DIFFRACTION98.77
2.61-2.660.28691450.23712715X-RAY DIFFRACTION99.31
2.66-2.710.31321320.22432734X-RAY DIFFRACTION98.83
2.71-2.770.25311480.21282726X-RAY DIFFRACTION99.83
2.77-2.840.28441540.20842728X-RAY DIFFRACTION99.07
2.84-2.910.24851220.2082746X-RAY DIFFRACTION99.79
2.91-2.990.27641430.20982745X-RAY DIFFRACTION99.31
2.99-3.070.24871480.20192733X-RAY DIFFRACTION99.69
3.07-3.170.25031590.20892727X-RAY DIFFRACTION99.62
3.17-3.290.2461600.19132756X-RAY DIFFRACTION99.35
3.29-3.420.21441160.1782743X-RAY DIFFRACTION99.79
3.42-3.570.21051500.17552752X-RAY DIFFRACTION99.66
3.57-3.760.24031500.17272734X-RAY DIFFRACTION99.28
3.76-3.990.20541660.15762718X-RAY DIFFRACTION99.62
3.99-4.30.18471560.1462747X-RAY DIFFRACTION99.55
4.3-4.730.16731890.1322754X-RAY DIFFRACTION99.66
4.73-5.410.16661360.14482738X-RAY DIFFRACTION99.48
5.42-6.810.24311340.17792795X-RAY DIFFRACTION99.59
6.81-29.640.14951230.1512753X-RAY DIFFRACTION96.12

+
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