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- PDB-4pom: Crystal structures of thioredoxin with mesna at 1.85A resolution -

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Basic information

Entry
Database: PDB / ID: 4pom
TitleCrystal structures of thioredoxin with mesna at 1.85A resolution
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


positive regulation of peptidyl-cysteine S-nitrosylation / Protein repair / cellular detoxification of hydrogen peroxide / 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 / positive regulation of DNA binding / NFE2L2 regulating anti-oxidant/detoxification enzymes ...positive regulation of peptidyl-cysteine S-nitrosylation / Protein repair / cellular detoxification of hydrogen peroxide / 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 / positive regulation of DNA binding / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / protein-disulfide reductase activity / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / 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 / cytoplasm / cytosol
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: 1.85 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,4896
Polymers48,2044
Non-polymers2842
Water4,252236
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1932
Polymers12,0511
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1932
Polymers12,0511
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,0511
Polymers12,0511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,0511
Polymers12,0511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-44 kcal/mol
Surface area20370 Å2
MethodPISA
6
A: Thioredoxin
hetero molecules

B: Thioredoxin
hetero molecules

C: Thioredoxin
D: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)48,4896
Polymers48,2044
Non-polymers2842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area4030 Å2
ΔGint-26 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.536, 91.776, 57.100
Angle α, β, γ (deg.)90.00, 105.36, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 28% PEG3350, 0.2M KCl, 160 mg/mL Trx protein, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 37414 / Num. obs: 37414 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3733 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4POK

4pok


Resolution: 1.85→36.11 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.83 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26141 1871 5 %RANDOM
Rwork0.21266 ---
obs0.21512 35518 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.139 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3249 0 14 236 3499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223352
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9554518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37826.364132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64915602
X-RAY DIFFRACTIONr_chiral_restr0.0960.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212444
X-RAY DIFFRACTIONr_mcbond_it1.15222128
X-RAY DIFFRACTIONr_mcangle_it1.9782.53433
X-RAY DIFFRACTIONr_scbond_it2.66931224
X-RAY DIFFRACTIONr_scangle_it4.2024.51085
LS refinement shellResolution: 1.855→1.903 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 134
Rwork0.296 2542

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