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

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Basic information

Entry
Database: PDB / ID: 2ifq
TitleCrystal structure of S-nitroso thioredoxin
Components(Thioredoxin) x 2
KeywordsOXIDOREDUCTASE / S-nitrosocysteine / phoroteduction
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
ETHANOL / Thioredoxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 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 21, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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
C: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4947
Polymers35,3093
Non-polymers1844
Water1,838102
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,7791
Polymers11,7791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7972
Polymers11,7501
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9184
Polymers11,7791
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.080, 25.749, 85.860
Angle α, β, γ (deg.)90.00, 97.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-118-

HOH

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Components

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


Mass: 11779.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: S-nitrosocysteine at position 69 / Source: (gene. exp.) Homo sapiens (human) / Gene: TXN, TRDX, TRX, TRX1 / Plasmid: pet-3a / Production host: Escherichia coli (E. coli) / References: UniProt: P10599
#2: Protein Thioredoxin / ATL-derived factor / ADF / Surface-associated sulphydryl protein / SASP


Mass: 11750.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: No modification at position 69 as a result of photoreduction of the SNO group
Source: (gene. exp.) Homo sapiens (human) / Gene: TXN, TRDX, TRX, TRX1 / Plasmid: pet-3a / Production host: Escherichia coli (E. coli) / References: UniProt: P10599
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.8 Å3/Da / Density % sol: 31.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 32% PEG 4000, 50 mM sodium phosphate, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2006 / Details: bent Si-mirror
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.2→25.1 Å / Num. all: 79717 / Num. obs: 79717 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.3 / Num. unique all: 7774 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDISPLAYFdata collection
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2HXK

2hxk


Resolution: 1.2→25.13 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.145 / SU ML: 0.024 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20565 3882 5 %RANDOM
Rwork0.17716 ---
obs0.17859 73521 97.1 %-
all-73521 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.03 Å2
2--0.25 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.2→25.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 0 115 2800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222771
X-RAY DIFFRACTIONr_bond_other_d0.0010.021891
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9653758
X-RAY DIFFRACTIONr_angle_other_deg0.99834711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51627.016124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11215531
X-RAY DIFFRACTIONr_chiral_restr0.1030.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023122
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02515
X-RAY DIFFRACTIONr_nbd_refined0.2760.2525
X-RAY DIFFRACTIONr_nbd_other0.1920.21815
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21340
X-RAY DIFFRACTIONr_nbtor_other0.1090.21469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3350.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.223
X-RAY DIFFRACTIONr_mcbond_it2.5481.52216
X-RAY DIFFRACTIONr_mcbond_other1.3741.5688
X-RAY DIFFRACTIONr_mcangle_it3.0722802
X-RAY DIFFRACTIONr_scbond_it4.27831219
X-RAY DIFFRACTIONr_scangle_it5.4994.5936
X-RAY DIFFRACTIONr_rigid_bond_restr2.65533407
X-RAY DIFFRACTIONr_sphericity_free11.053398
X-RAY DIFFRACTIONr_sphericity_bonded5.50832674
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 311 -
Rwork0.162 5468 -
obs-5468 98.5 %

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