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- PDB-1o8x: Mutant tryparedoxin-I Cys43Ala -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1o8x
TitleMutant tryparedoxin-I Cys43Ala
ComponentsTRYPAREDOXIN
KeywordsELECTRON TRANSPORT / TRYPAREDOXIN-I / SYNCHROTRON RADIATION / DISULFIDE BONDS TRYPAREDOXIN / CRITHIDIA FASCICULATA / THIOREDOXIN / TRYPANOSOME / ANOMALOUS DISPERSION / OXIDATIVE STRESS / OXIDOREDUCTASE
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / negative regulation of protein ubiquitination / nucleus
Similarity search - Function
TryX and NRX, thioredoxin domain / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCRITHIDIA FASCICULATA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsAlphey, M.S. / Bond, C.S. / Hunter, W.N.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Tryparedoxins from Crithidia Fasciculata and Trypanosoma Brucei: Photoreduction of the Redox Disulfide Using Synchrotron Radiation and Evidence for a Conformational Switch Implicated in Function
Authors: Alphey, M.S. / Gabrielsen, M. / Micossi, E. / Leonard, G. / Mcsweeney, S.M. / Ravelli, R.B.G. / Tetaud, E. / Fairlamb, A.H. / Bond, C.S. / Hunter, W.N.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: The High Resolution Structure of Recombinant Crithidia Fasciculata Tryparedoxin-I
Authors: Alphey, M.S. / Leonard, G. / Gourley, D.G. / Tetaud, E. / Fairlamb, A.H. / Hunter, W.N.
History
DepositionDec 9, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPAREDOXIN


Theoretical massNumber of molelcules
Total (without water)16,4671
Polymers16,4671
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.699, 50.934, 70.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPAREDOXIN / TRYX / TXNI


Mass: 16466.568 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRITHIDIA FASCICULATA (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O96438
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION CYS 43 ALA

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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: 2.17 Å3/Da / Density % sol: 42.8 %
Crystal growpH: 8.2 / Details: pH 8.20
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Alphey, M.S., (1999) J. Struct. Biol., 126, 76.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.0 mg/mlprotein1drop
230 %PEG2000 MME1reservoir
30.1 MTris-HCl1reservoirpH8.2
41 %dimethyl sulfoxide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 35022 / % possible obs: 96.6 % / Redundancy: 2 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.045 / Net I/σ(I): 18.6
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.439 / % possible all: 88.9
Reflection
*PLUS
Redundancy: 7.5 % / Num. measured all: 261452 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.439

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1QK8

1qk8


Resolution: 1.3→28.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.926 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1715 5.1 %RANDOM
Rwork0.175 ---
obs0.177 32098 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 21.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 0 214 1358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211179
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9411598
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5345142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.2559
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1951.5713
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99321146
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6443466
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9564.5452
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 128
Rwork0.24 2097
Software
*PLUS
Name: REFMAC / Version: 5.1.19 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.228 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6
LS refinement shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.33 Å / Rfactor Rfree: 0.265 / Num. reflection Rfree: 128 / Rfactor Rwork: 0.24 / Num. reflection Rwork: 2097 / Total num. of bins used: 20

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