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- PDB-1o85: Radiation-reduced Tryparedoxin-I -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1o85
TitleRadiation-reduced Tryparedoxin-I
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: 1.5 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 Crystal 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
DepositionNov 25, 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
Revision 1.4Nov 6, 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: TRYPAREDOXIN


Theoretical massNumber of molelcules
Total (without water)16,4991
Polymers16,4991
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.060, 50.885, 70.703
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: 16498.633 Da / Num. of mol.: 1
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 / References: UniProt: O96438
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.41 Å3/Da / Density % sol: 42 %
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: 1.5→50 Å / Num. obs: 22753 / % possible obs: 94 % / Redundancy: 2 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.5 / % possible all: 76.3
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / % possible obs: 94.5 % / Redundancy: 7.4 % / Num. measured all: 167593
Reflection shell
*PLUS
% possible obs: 76.3 % / Rmerge(I) obs: 0.395

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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: 1.5→41.17 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.656 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1131 5.2 %RANDOM
Rwork0.195 ---
obs0.198 20641 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: 24.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 0 128 1272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.4241.9421599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
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_restr5.6635142
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2536
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2720.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5691.5713
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54621147
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3443467
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7924.5452
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 60
Rwork0.22 1282
Software
*PLUS
Name: REFMAC / Version: 5.1.19 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.266 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.54 Å / Rfactor Rfree: 0.254 / Num. reflection Rfree: 60 / Rfactor Rwork: 0.22 / Num. reflection Rwork: 1282 / Total num. of bins used: 20

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