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- PDB-4oo4: Crystal Structure of Human Thioredoxin Mutant -

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Basic information

Entry
Database: PDB / ID: 4oo4
TitleCrystal Structure of Human Thioredoxin Mutant
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / S-nitrosation
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: 0.97 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 27, 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
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)23,3232
Polymers23,3232
Non-polymers00
Water6,125340
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.269, 50.182, 51.066
Angle α, β, γ (deg.)90.00, 94.08, 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: 11661.297 Da / Num. of mol.: 2 / Mutation: Q63A, 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.: 340 / 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: 1.93 Å3/Da / Density % sol: 36.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% PEG 3350, 0.1 M sodium acetate, 2 mM DTT, pH 4.0, 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: 0.9796 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2011 / 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: 0.9796 Å / Relative weight: 1
ReflectionResolution: 0.97→50.94 Å / Num. all: 88291 / Num. obs: 88291 / % possible obs: 84.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 18.8
Reflection shellResolution: 0.97→1.02 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.6 / % possible all: 44.5

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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: 0.97→35.75 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.991 / SU ML: 0.024 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16498 4412 5 %RANDOM
Rwork0.13582 ---
obs0.13726 83851 84.1 %-
all-83851 --
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: 14.371 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å2-1.25 Å2
2--1.51 Å20 Å2
3----0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.133 Å
Refinement stepCycle: LAST / Resolution: 0.97→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 0 340 1974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192346
X-RAY DIFFRACTIONr_bond_other_d0.0030.022189
X-RAY DIFFRACTIONr_angle_refined_deg1.991.9553199
X-RAY DIFFRACTIONr_angle_other_deg1.02135143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.927100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12615448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022797
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02497
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_it1.7921.0621196
X-RAY DIFFRACTIONr_mcbond_other1.7891.0611195
X-RAY DIFFRACTIONr_mcangle_it2.3661.6071544
X-RAY DIFFRACTIONr_mcangle_other2.2951.6191535
X-RAY DIFFRACTIONr_scbond_it2.511.321150
X-RAY DIFFRACTIONr_scbond_other2.421.3171137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6971.8641636
X-RAY DIFFRACTIONr_long_range_B_refined10.59712.6132826
X-RAY DIFFRACTIONr_long_range_B_other7.01110.3852620
X-RAY DIFFRACTIONr_rigid_bond_restr5.26434534
X-RAY DIFFRACTIONr_sphericity_free54.765557
X-RAY DIFFRACTIONr_sphericity_bonded21.46954773
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 148 -
Rwork0.337 2870 -
obs--39.15 %

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