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- PDB-1o81: Tryparedoxin II from C.fasciculata solved by sulphur phasing -

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Basic information

Entry
Database: PDB / ID: 1o81
TitleTryparedoxin II from C.fasciculata solved by sulphur phasing
ComponentsTRYPAREDOXIN II
KeywordsELECTRON TRANSPORT / TRYPAREDOXIN II / SULPHUR PHASING / SAD / S-SAD
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 / OTHER / Resolution: 1.5 Å
AuthorsLeonard, G.A. / Micossi, E. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: De Novo Phasing of Two Crystal Forms of Tryparedoxin II Using the Anomalous Scattering from S Atoms: A Combination of Small Signal and Medium Resolution Reveals This to be a General Tool for ...Title: De Novo Phasing of Two Crystal Forms of Tryparedoxin II Using the Anomalous Scattering from S Atoms: A Combination of Small Signal and Medium Resolution Reveals This to be a General Tool for Solving Protein Crystal Structures
Authors: Micossi, E. / Hunter, W.N. / Leonard, G.A.
History
DepositionNov 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 9, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf
Revision 1.5Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water6,017334
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
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
Unit cell
Length a, b, c (Å)111.700, 111.700, 56.500
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-2012-

HOH

21A-2077-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3608, 0.3246, -0.8743), (0.7161, -0.697, 0.0367), (-0.5975, -0.6393, -0.484)
Vector: -6.2051, 15.2726, 47.9702)

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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 (E. coli) / Strain (production host): BL21(DE3) / 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.: 334 / 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 growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.77
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 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 / Rsym value: 0.045 / Net I/σ(I): 37.6
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.354 / % possible all: 95.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: OTHER / Resolution: 1.5→40 Å / SU B: 1.96 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.077 / Details: CNS USED IN INITIAL STAGES
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 2929 5.1 %RANDOM
Rwork0.20815 ---
obs0.20914 54679 99.77 %-
Displacement parametersBiso mean: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 5 334 2697

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