[English] 日本語
Yorodumi
- PDB-4ccr: Crystal structure of the thioredoxin reductase apoenzyme from Ent... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ccr
TitleCrystal structure of the thioredoxin reductase apoenzyme from Entamoeba histolytica in the absence of the NADP cofactor
ComponentsTHIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / AMOEBIASIS / REDOX METABOLISM / OXIDATIVE STRESS / AURANOFIN
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / nucleotide binding / cytosol
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesENTAMOEBA HISTOLYTICA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsParsonage, D. / Kells, P.M. / Hirata, K. / Debnath, A. / Poole, L.B. / McKerrow, J.H. / Reed, S.L. / Podust, L.M.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: X-Ray Structures of Thioredoxin and Thioredoxin Reductase from Entamoeba Histolytica and Prevailing Hypothesis of the Mechanism of Auranofin Action.
Authors: Parsonage, D. / Sheng, F. / Hirata, K. / Debnath, A. / Mckerrow, J.H. / Reed, S.L. / Abagyan, R. / Poole, L.B. / Podust, L.M.
History
DepositionOct 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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 REDUCTASE
B: THIOREDOXIN REDUCTASE
C: THIOREDOXIN REDUCTASE
D: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,04812
Polymers135,1184
Non-polymers3,9308
Water4,270237
1
A: THIOREDOXIN REDUCTASE
C: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5246
Polymers67,5592
Non-polymers1,9654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-50 kcal/mol
Surface area24240 Å2
MethodPISA
2
B: THIOREDOXIN REDUCTASE
D: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5246
Polymers67,5592
Non-polymers1,9654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-44.8 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.777, 91.029, 90.152
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
THIOREDOXIN REDUCTASE


Mass: 33779.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTAMOEBA HISTOLYTICA (eukaryote) / Plasmid: PTRCHISA / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834
References: UniProt: C4LW95, thioredoxin-disulfide reductase (NADPH)
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsGOLD ION (AU): GOLD IS RELEASED BY AURANOFIN PRESENT IN CRYSTALLIZATION CONDITIONS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.46 %
Description: ISOLATED FAD- AND NADPH-BINDING DOMAINS OF SACCHAROMYCES CEREVISIAE THIOREDOXIN REDUCTASE WERE USED AS SEARCH MODELS
Crystal growpH: 7
Details: 20% PEG 3350,0.2 M AMMONIUM TARTRATE, PH 7.0; 3 MM AURANOFIN

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 29, 2013 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.28→91.03 Å / Num. obs: 59359 / % possible obs: 99.7 % / Observed criterion σ(I): 0.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ITJ

3itj


Resolution: 2.28→91.03 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.016 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTIRE NADPH-BINDING DOMAIN IN CHAIN D IS OMITTED FROM THE STRUCTURE DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26526 2992 5 %RANDOM
Rwork0.20282 ---
obs0.20598 56315 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.674 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20.26 Å2
2--1.16 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.28→91.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8392 0 216 237 8845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198789
X-RAY DIFFRACTIONr_bond_other_d0.0010.028257
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9811953
X-RAY DIFFRACTIONr_angle_other_deg0.8243.00118996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49751121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35724.567335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.756151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0321532
X-RAY DIFFRACTIONr_chiral_restr0.0860.21355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021918
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_it3.0014.2364502
X-RAY DIFFRACTIONr_mcbond_other2.9994.2364501
X-RAY DIFFRACTIONr_mcangle_it4.346.3455617
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3634.5534287
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 248 -
Rwork0.3 4117 -
obs--99.68 %

+
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