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- PDB-1o73: Tryparedoxin from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 1o73
TitleTryparedoxin from Trypanosoma brucei
ComponentsTRYPAREDOXIN
KeywordsELECTRON TRANSPORT / TRYPAREDOXIN / TRYPANOSOMATID / TRYPANOSOMA BRUCEI / THIOREDOXIN
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, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...TryX and NRX, thioredoxin domain / Thioredoxin-like / Thioredoxin-like fold / 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 speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsGabrielsen, M. / Alphey, M.S. / Bond, C.S. / Hunter, W.N.
CitationJournal: 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.A. / Mcsweeney, S.M. / Ravelli, R.B.G. / Tetaud, E. / Fairlamb, A.H. / Bond, C.S. / Hunter, W.N.
History
DepositionOct 23, 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPAREDOXIN


Theoretical massNumber of molelcules
Total (without water)15,9051
Polymers15,9051
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.600, 31.460, 56.930
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRYPAREDOXIN


Mass: 15904.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 427 / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O77404
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN PARTICIPATES IN VARIOUS REDOX REACTIONS BY THE REVERSIBLE OXIDATION OF ITS ACTIVE ...THIS PROTEIN PARTICIPATES IN VARIOUS REDOX REACTIONS BY THE REVERSIBLE OXIDATION OF ITS ACTIVE CENTER DITHIOL TO A DISULFIDE. IT ALSO CATALYZES DITHIOL-DISULFIDE EXCHANGE REACTIONS.
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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.6
Details: 50 MM HEPES PH 7.5, 30% PEG4000, 100 MM SODIUM ACETATE PH 4.6, 200 MM AMMONIUM ACETATE
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMHEPES1droppH7.5
330 %PEG40001reservoir
4100 mMsodium acetate1reservoirpH4.6
5200 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: ROTATING ANODE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→56.8 Å / Num. obs: 5030 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.6
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 6.5 / % possible all: 94.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 4699 / Num. measured all: 37965
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QK8

1qk8


Resolution: 2.28→56.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.827 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.802 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 229 4.6 %RANDOM
Rwork0.177 ---
obs-4794 98.6 %-
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: 26.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20.45 Å2
2---0.95 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.28→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 63 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0490.0211159
X-RAY DIFFRACTIONr_bond_other_d0.0020.021018
X-RAY DIFFRACTIONr_angle_refined_deg3.041.9451581
X-RAY DIFFRACTIONr_angle_other_deg1.36132376
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_restr0.2070.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.020.021292
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02240
X-RAY DIFFRACTIONr_nbd_refined0.2180.2221
X-RAY DIFFRACTIONr_nbd_other0.2470.21097
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.110.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8241.5718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.85421161
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2713441
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9954.5420
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: 2.28→2.34 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 23
Rwork0.204 324
Software
*PLUS
Name: REFMAC / Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.45
LS refinement shell
*PLUS
Highest resolution: 2.28 Å / Lowest resolution: 2.34 Å / Rfactor Rfree: 0.247 / Num. reflection Rfree: 23 / Rfactor Rwork: 0.204 / Num. reflection Rwork: 324 / Total num. of bins used: 20

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