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- PDB-3m9k: Crystal structure of human thioredoxin C69/73S double-mutant, oxi... -

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Basic information

Entry
Database: PDB / ID: 3m9k
TitleCrystal structure of human thioredoxin C69/73S double-mutant, oxidized form
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / dimer / intermolecular disulfide bond / DTT / disulfide bond / S-nitrosylation
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 / 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
(4S,5S)-1,2-DITHIANE-4,5-DIOL / Thioredoxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
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.
#1: Journal: Biochemistry / Year: 2007
Title: Buried S-nitrosocysteine revealed in crystal structures of human thioredoxin.
Authors: Weichsel, A. / Brailey, J.L. / Montfort, W.R.
#2: Journal: Structure / Year: 1996
Title: Crystal structures of reduced, oxidized, and mutated human thioredoxins: evidence for a regulatory homodimer.
Authors: Weichsel, A. / Gasdaska, J.R. / Powis, G. / Montfort, W.R.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9737
Polymers23,4372
Non-polymers5365
Water2,972165
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8142
Polymers11,7181
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1595
Polymers11,7181
Non-polymers4404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Thioredoxin
B: Thioredoxin
hetero molecules

A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,94614
Polymers46,8734
Non-polymers1,07310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area3510 Å2
ΔGint-20 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.620, 125.620, 33.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

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


Mass: 11718.348 Da / Num. of mol.: 2 / Mutation: C69S, C73S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXN, TRDX, TRX, TRX1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P10599
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 1.8 M ammonium sulfate, 100 mM MES, 10 mM CoCl2, 2 mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2009 / 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→22.43 Å / Num. obs: 48316 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 9.89 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9.16 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.8 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERT

1ert


Resolution: 1.5→22.34 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.812 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2445 5.1 %RANDOM
Rwork0.184 ---
obs0.185 48316 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.32 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: LAST / Resolution: 1.5→22.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 28 165 1835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221945
X-RAY DIFFRACTIONr_bond_other_d0.0010.021325
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9722658
X-RAY DIFFRACTIONr_angle_other_deg0.953.0043303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67127.01187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51915373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022227
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02363
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6641.51191
X-RAY DIFFRACTIONr_mcbond_other0.7631.5471
X-RAY DIFFRACTIONr_mcangle_it2.54721960
X-RAY DIFFRACTIONr_scbond_it3.7243754
X-RAY DIFFRACTIONr_scangle_it5.544.5685
X-RAY DIFFRACTIONr_rigid_bond_restr1.80733270
X-RAY DIFFRACTIONr_sphericity_free9.1923167
X-RAY DIFFRACTIONr_sphericity_bonded3.53133212
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 164 -
Rwork0.303 3296 -
obs--97.05 %

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