[English] 日本語
Yorodumi
- PDB-4pol: Crystal structures of thioredoxin with mesna at 2.8A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pol
TitleCrystal structures of thioredoxin with mesna at 2.8A resolution
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide ...Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / positive regulation of DNA binding / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-THIOETHANESULFONIC ACID / Thioredoxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSridhar, V. / Chie-Leon, B. / Badger, J. / Nienaber, V.L. / Hausheer, F.H.
CitationJournal: J Pharmacol Clin Toxicol / Year: 2014
Title: BNP7787 Forms Novel Covalent Adducts on Human Thioredoxin and Modulates Thioredoxin Activity
Authors: Parker, A.R. / Nienaber, V.L. / Petluru, P.N. / Sridhar, V. / Leverett, B.D. / Ayala, P.Y. / Zhao, M. / Chie-Leon, B. / Jair, K. / Kochat, H. / Badger, J. / Hausheer, F.H.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
C: Thioredoxin
D: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7738
Polymers48,2044
Non-polymers5694
Water0
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3353
Polymers12,0511
Non-polymers2842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3353
Polymers12,0511
Non-polymers2842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,0511
Polymers12,0511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,0511
Polymers12,0511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Thioredoxin
hetero molecules

B: Thioredoxin
hetero molecules

C: Thioredoxin
D: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)48,7738
Polymers48,2044
Non-polymers5694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_566x,y+1,z+11
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area4640 Å2
ΔGint-28 kcal/mol
Surface area21880 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-48 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.478, 57.923, 94.902
Angle α, β, γ (deg.)90.00, 90.34, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Thioredoxin / / Trx / ATL-derived factor / ADF / Surface-associated sulphydryl protein / SASP


Mass: 12051.055 Da / Num. of mol.: 4 / Mutation: E13K, D16K, E95K, E103K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXN, TRDX, TRX, TRX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10599
#2: Chemical
ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O3S2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2 M KCl, 60 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.8→48 Å / Num. all: 11124 / Num. obs: 11124 / % possible obs: 96.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1533 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PO4

4po4


Resolution: 2.8→47.95 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.827 / SU B: 18.543 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31232 531 4.8 %RANDOM
Rwork0.24475 ---
obs0.24794 10588 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0.08 Å2
2---0.02 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 28 0 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223381
X-RAY DIFFRACTIONr_angle_refined_deg0.8851.9684558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6585420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21426.496137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7115615
X-RAY DIFFRACTIONr_chiral_restr0.0580.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212448
X-RAY DIFFRACTIONr_mcbond_it0.33922112
X-RAY DIFFRACTIONr_mcangle_it0.6252.53402
X-RAY DIFFRACTIONr_scbond_it0.52131269
X-RAY DIFFRACTIONr_scangle_it0.9174.51156
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.504 38
Rwork0.353 740

+
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