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- PDB-1oc8: TRYPAREDOXIN II FROM C.FASCICULATA SOLVED BY MR -

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Basic information

Entry
Database: PDB / ID: 1oc8
TitleTRYPAREDOXIN II FROM C.FASCICULATA SOLVED BY MR
ComponentsTRYPAREDOXIN II
KeywordsELECTRON TRANSPORT / TRYPAREDOXIN II
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLeonard, G.A. / Micossi, E. / 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
DepositionFeb 7, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_special_symmetry
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 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 1.5Nov 13, 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: TRYPAREDOXIN II
B: TRYPAREDOXIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4243
Polymers34,3272
Non-polymers961
Water5,675315
1
A: TRYPAREDOXIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2602
Polymers17,1641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TRYPAREDOXIN II


Theoretical massNumber of molelcules
Total (without water)17,1641
Polymers17,1641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.745, 111.745, 56.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

21A-2076-

HOH

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Components

#1: Protein TRYPAREDOXIN II


Mass: 17163.721 Da / Num. of mol.: 2 / Fragment: RESIDUES 14-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRITHIDIA FASCICULATA (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: O77093
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
215 %(w/v)PEG80001reservoir
330 mMsodium cacodylate1reservoirpH6.5
45 mMdithiothreitol1reservoir
560 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.977
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 57687 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 37.6
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.1 / % possible all: 95.5
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 40 Å / Num. measured all: 469429
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.354

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QK8

1qk8


Resolution: 1.5→40 Å / SU B: 1.992 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / Details: CNS USED IN INITIAL STAGES
RfactorNum. reflection% reflectionSelection details
Rfree0.23455 2929 5.1 %RANDOM
Rwork0.20993 ---
obs0.21118 54679 99.77 %-
Displacement parametersBiso mean: 19.265 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 5 315 2627
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.86

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