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- PDB-3m9j: Crystal structure of human thioredoxin C69/73S double mutant, red... -

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Basic information

Entry
Database: PDB / ID: 3m9j
TitleCrystal structure of human thioredoxin C69/73S double mutant, reduced form
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / 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 / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide ...Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / 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 / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / positive regulation of DNA binding / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / 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 / molecular replacement / Resolution: 1.1 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 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)23,4372
Polymers23,4372
Non-polymers00
Water3,909217
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,7181
Polymers11,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,7181
Polymers11,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.233, 46.207, 52.330
Angle α, β, γ (deg.)90.00, 93.25, 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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 30% PEG 4000, 200 mM ammonium acetate, 100 mM sodium citrate, 5 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 18, 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: 1.1→30 Å / Num. obs: 69644 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 40
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.2 / % possible all: 91.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERT

1ert


Resolution: 1.1→17.83 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.88 / SU ML: 0.02 / SU R Cruickshank DPI: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.172 3536 5.1 %RANDOM
Rwork0.144 ---
obs0.145 69636 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.03 Å2
2---0.1 Å20 Å2
3----0.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.137 Å
Refinement stepCycle: LAST / Resolution: 1.1→17.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 0 217 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222005
X-RAY DIFFRACTIONr_bond_other_d0.0010.021352
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9592736
X-RAY DIFFRACTIONr_angle_other_deg0.93633371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54526.89787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64515382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022351
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
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_it1.8491.51261
X-RAY DIFFRACTIONr_mcbond_other0.6261.5498
X-RAY DIFFRACTIONr_mcangle_it2.75722076
X-RAY DIFFRACTIONr_scbond_it4.0993744
X-RAY DIFFRACTIONr_scangle_it6.1284.5658
X-RAY DIFFRACTIONr_rigid_bond_restr1.63233357
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 220 -
Rwork0.306 4495 -
obs--89.4 %

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