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- PDB-3kd0: Human thioredoxin C35S,C62S,C69S,C73S mutant showing cadmium chlo... -

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Basic information

Entry
Database: PDB / ID: 3kd0
TitleHuman thioredoxin C35S,C62S,C69S,C73S mutant showing cadmium chloride bound to the active site
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / Thioredoxin Fold / Disulfide bond / Electron transport / Redox-active center / Transport
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 / Resolution: 1.7 Å
AuthorsHall, G. / Emsley, J.
CitationJournal: To be Published
Title: The 1.7 A resolution crystal structure of a cadmium chloride complex with the active site of a mutant human thioredoxin
Authors: Hall, G. / Emsley, J.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 1.3Nov 1, 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

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Assembly

Deposited unit
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9406
Polymers11,6861
Non-polymers2545
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Thioredoxin
hetero molecules

A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,88112
Polymers23,3722
Non-polymers50810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1810 Å2
ΔGint-89 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.635, 53.635, 154.148
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

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Components

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


Mass: 11686.217 Da / Num. of mol.: 1 / Mutation: C35S, C62S, C69S, C73S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hTrx-1, TRDX, TRX, TRX1, TXN / Plasmid: pETBlue-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: P10599
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.16M Cadmium Chloride, 2.0M ammonium sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2007
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→26.9 Å / Num. all: 15248 / Num. obs: 15248 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.1 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 29.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2184 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERT

1ert


Resolution: 1.7→23.22 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.891 / SU B: 2.634 / SU ML: 0.088 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27903 764 5 %RANDOM
Rwork0.23208 ---
all0.247 14482 --
obs0.23431 14482 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.382 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 5 76 893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022877
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9521190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09126.97743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85815167
X-RAY DIFFRACTIONr_chiral_restr0.130.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021665
X-RAY DIFFRACTIONr_mcbond_it1.3981.5538
X-RAY DIFFRACTIONr_mcangle_it2.252876
X-RAY DIFFRACTIONr_scbond_it3.5553339
X-RAY DIFFRACTIONr_scangle_it5.5694.5307
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 54 -
Rwork0.272 1018 -
obs-42249 100 %

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