[English] 日本語
Yorodumi
- PDB-2x99: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x99
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with NADPH
ComponentsTHIOREDOXIN GLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / THIOREDOXIN / GLUTATHIONE / NADPH / DETOXIFICATION PATHWAY
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 / FAD/NAD-linked reductase, C-terminal dimerisation domain ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / GLUTATHIONE / Chem-NDP / DI(HYDROXYETHYL)ETHER / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsAngelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Mapping the Catalytic Cycle of Schistosoma Mansoni Thioredoxin Glutathione Reductase by X-Ray Crystallography
Authors: Angelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A.
#1: Journal: Proteins / Year: 2008
Title: Glutathione Reductase and Thioredoxin Reductase at the Crossroad: The Structure of Schistosoma Mansoni Thioredoxin Glutathione Reductase.
Authors: Angelucci, F. / Miele, A.E. / Boumis, G. / Dimastrogiovanni, D. / Brunori, M. / Bellelli, A.
#2: Journal: J.Biol.Chem. / Year: 2009
Title: Inhibition of Schistosoma Mansoni Thioredoxin- Glutathione Reductase by Auranofin: Structural and Kinetic Aspects.
Authors: Angelucci, F. / Sayed, A.A. / Williams, D.L. / Boumis, G. / Brunori, M. / Dimastrogiovanni, D. / Miele, A.E. / Pauly, F. / Bellelli, A.
History
DepositionMar 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Jul 12, 2017Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,85517
Polymers65,0611
Non-polymers3,79416
Water3,333185
1
A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules

A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,70934
Polymers130,1222
Non-polymers7,58732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area23260 Å2
ΔGint-37.7 kcal/mol
Surface area45690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.502, 102.610, 59.938
Angle α, β, γ (deg.)90.00, 112.82, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein THIOREDOXIN GLUTATHIONE REDUCTASE


Mass: 65061.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q962Y6, EC: 1.6.4.5

-
Non-polymers , 7 types, 201 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsRESIDUE 597 IS GIVEN AS X IN UNIPROT, IT IS CYS IN THIS CONSTRUCT

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.16 % / Description: 2V6O USED AS STARTING MODEL
Crystal growpH: 7.4
Details: 0.1 M HEPES AT PH 7.0, 20% PEG 3350, 0.2 M KSCN, 5 MM GSH, 0.4 MM NADPH.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 33294 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
PDBSETphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.246 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. RESIDUES 1-5 AND 593-598 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. RESIDUES 1-5 AND 593-598 OF CHAIN A ARE NOT VISIBLE BY THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.23119 1743 5 %RANDOM
Rwork0.18971 ---
obs0.19176 33294 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.527 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å2-0.58 Å2
2---3.33 Å20 Å2
3---4.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 249 185 4930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224837
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3022.0116526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22824.865185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55715800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3751517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213485
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5161.52906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98724688
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.62531931
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6784.51836
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 120 -
Rwork0.219 2440 -
obs--99.73 %
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)
14.46390.5867-2.77782.6999-0.43784.2689-0.20470.32890.3671-0.32180.18380.4253-0.12580.05320.02090.1057-0.0823-0.05230.0760.04260.238132.10829.86-5.309
21.66741.8237-0.92122.244-1.42241.2381-0.0419-0.00150.0908-0.1002-0.01490.06490.06230.05280.05670.1031-0.02010.01430.0587-0.0280.172238.6624.970.724
31.97280.25831.11860.4135-0.1330.8831-0.0056-0.1049-0.0314-0.06120.03710.03350.0474-0.0476-0.03150.11130.0294-0.00520.0793-0.02120.145512.029-10.028.489
41.20351.2242-0.68781.4656-0.88860.9332-0.0149-0.1152-0.01810.0121-0.0114-0.12180.07530.13620.02630.07660.0474-0.02050.1341-0.05450.145129.392.80118.572
51.4891-1.04020.53861.7758-1.13311.0412-0.1072-0.20880.07310.01170.0796-0.06910.0336-0.08440.02750.09880.04140.00240.1109-0.0180.07973.76-8.97626.298
60.82050.6061-0.17740.78980.00940.1860.0573-0.09860.19490.0957-0.01170.0935-0.00150.0447-0.04560.09080.007-0.01750.076-0.06790.167218.93814.50117.647
70.71150.19950.07921.0307-0.07340.9721-0.0159-0.06610.1279-0.00240.06210.0627-0.0239-0.087-0.04620.06980.0341-0.00390.0396-0.00740.189-7.2912.769.855
81.1531-0.5482-1.40461.1323-0.09814.2135-0.02580.0461-0.05140.0091-0.05020.3710.0341-0.10690.07610.0714-0.0255-0.00740.06220.00180.3052-13.94311.6554.035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 58
2X-RAY DIFFRACTION2A59 - 136
3X-RAY DIFFRACTION3A137 - 211
4X-RAY DIFFRACTION4A212 - 284
5X-RAY DIFFRACTION5A285 - 385
6X-RAY DIFFRACTION6A386 - 478
7X-RAY DIFFRACTION7A479 - 565
8X-RAY DIFFRACTION8A566 - 592

+
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