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- PDB-4oo5: Crystal Structure of S-nitrosated Human Thioredoxin Mutant -

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Basic information

Entry
Database: PDB / ID: 4oo5
TitleCrystal Structure of S-nitrosated Human Thioredoxin Mutant
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsThe, J. / Weichsel, A. / Montfort, W.R.
Citation
Journal: To be Published
Title: Crystal Structure of a Thioredoxin Mutant Displays a Dynamic N-terminal Loop Surrounding an S-nitrosation Site
Authors: The, J. / Weichsel, A. / Montfort, W.R.
#1: Journal: Protein Sci. / Year: 2010
Title: Crystal structure of human thioredoxin revealing an unraveled helix and exposed S-nitrosation site.
Authors: Weichsel, A. / Kem, M. / Montfort, W.R.
History
DepositionJan 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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
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 1.2Oct 16, 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)11,7471
Polymers11,7471
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.008, 26.038, 51.090
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

21A-274-

HOH

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Components

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


Mass: 11747.345 Da / Num. of mol.: 1 / Mutation: C69S, C73S
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) / Strain (production host): BL21(DE3) / References: UniProt: P10599
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 1.89 Å3/Da / Density % sol: 34.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 21% PEG 3350, 0.1 M sodium acetate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 2012 / Details: RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.54→25.45 Å / Num. all: 12978 / Num. obs: 12978 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.2
Reflection shellResolution: 1.54→1.63 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1837 / % possible all: 95.9

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERT

1ert


Resolution: 1.54→25.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.969 / SU ML: 0.101 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24836 632 4.9 %RANDOM
Rwork0.19131 ---
obs0.19396 12317 98.2 %-
all-12317 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.765 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.17 Å2
2--1.63 Å20 Å2
3----1.64 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: LAST / Resolution: 1.54→25.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms823 0 0 101 924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019963
X-RAY DIFFRACTIONr_bond_other_d0.0010.02902
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.9681313
X-RAY DIFFRACTIONr_angle_other_deg0.93632122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3785132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6426.78642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36715189
X-RAY DIFFRACTIONr_chiral_restr0.1290.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021155
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02203
X-RAY DIFFRACTIONr_mcbond_it2.472.711489
X-RAY DIFFRACTIONr_mcbond_other2.4652.709488
X-RAY DIFFRACTIONr_mcangle_it3.3714.054634
X-RAY DIFFRACTIONr_mcangle_other3.3684.056635
X-RAY DIFFRACTIONr_scbond_it3.8793.028472
X-RAY DIFFRACTIONr_scbond_other3.8773.029472
X-RAY DIFFRACTIONr_scangle_other5.7434.404678
X-RAY DIFFRACTIONr_long_range_B_refined7.36622.8481162
X-RAY DIFFRACTIONr_long_range_B_other7.30822.3861128
LS refinement shellResolution: 1.544→1.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 43 -
Rwork0.302 816 -
obs-816 90.04 %

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