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- PDB-4pol: Crystal structures of thioredoxin with mesna at 2.8A resolution -

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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 / protein-disulfide reductase [NAD(P)H] activity / positive regulation of peptidyl-cysteine S-nitrosylation / 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 ...Protein repair / cellular detoxification of hydrogen peroxide / protein-disulfide reductase [NAD(P)H] activity / positive regulation of peptidyl-cysteine S-nitrosylation / 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 / The NLRP3 inflammasome / protein-disulfide reductase activity / Purinergic signaling in leishmaniasis infection / positive regulation of peptidyl-serine phosphorylation / 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 / 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
Revision 1.3Nov 27, 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)48,7738
Polymers48,2044
Non-polymers5694
Water00
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

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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.: 4 / Source method: obtained synthetically / Formula: C2H6O3S2
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: 2.44 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

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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

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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

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