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- PDB-2iiy: Crystal structure of S-nitroso thioredoxin -

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Basic information

Entry
Database: PDB / ID: 2iiy
TitleCrystal structure of S-nitroso thioredoxin
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / S-nitrosation / S-nitrosocysteine
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
Journal: Biochemistry / Year: 2007
Title: Buried s-nitrosocysteine revealed in crystal structures of human thioredoxin.
Authors: Weichsel, A. / Brailey, J.L. / Montfort, W.R.
#1: Journal: Structure / Year: 1996
Title: Crystal structures of reduced, oxidized, and mutated human thioredoxin: evidence for a regulatory homodimer
Authors: Weichsel, A. / Gasdaska, J.R. / Powis, G. / Montfort, W.R.
History
DepositionSep 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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
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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,8081
Polymers11,8081
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.860, 26.240, 51.300
Angle α, β, γ (deg.)90.00, 95.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-155-

HOH

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Components

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


Mass: 11808.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXN, TRDX, TRX, TRX1 / Plasmid: pet-3a / Production host: Escherichia coli (E. coli) / References: UniProt: P10599
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.9 Å3/Da / Density % sol: 35.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 32% PEG 1500, 50 mM sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 23, 2006 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→22.3 Å / Num. all: 9820 / Num. obs: 9820 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.2 / Num. unique all: 991 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1ERT

1ert


Resolution: 1.7→23 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.962 / SU ML: 0.098 / Isotropic thermal model: iotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23908 499 5.1 %RANDOM
Rwork0.20876 ---
all0.21024 9319 --
obs0.21024 9319 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.22 Å2
2--1.15 Å20 Å2
3----1.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: LAST / Resolution: 1.7→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 80 1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022949
X-RAY DIFFRACTIONr_bond_other_d0.0010.02650
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9691289
X-RAY DIFFRACTIONr_angle_other_deg1.1653.0021621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9727.14342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42915184
X-RAY DIFFRACTIONr_chiral_restr0.1120.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021101
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02178
X-RAY DIFFRACTIONr_nbd_refined0.2190.2194
X-RAY DIFFRACTIONr_nbd_other0.1770.2617
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2441
X-RAY DIFFRACTIONr_nbtor_other0.0830.2447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5450.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.212
X-RAY DIFFRACTIONr_mcbond_it1.271.5781
X-RAY DIFFRACTIONr_mcbond_other0.2621.5234
X-RAY DIFFRACTIONr_mcangle_it1.4762969
X-RAY DIFFRACTIONr_scbond_it2.3973419
X-RAY DIFFRACTIONr_scangle_it3.4344.5317
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 34 -
Rwork0.312 639 -
obs-639 92.83 %

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