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- PDB-1o6j: Tryparedoxin II from C.fasciculata solved by sulphur phasing -

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Basic information

Entry
Database: PDB / ID: 1o6j
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: 2.35 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
DepositionOct 4, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

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Assembly

Deposited unit
A: TRYPAREDOXIN II
B: TRYPAREDOXIN II


Theoretical massNumber of molelcules
Total (without water)33,8572
Polymers33,8572
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.200, 114.200, 102.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

21A-2030-

HOH

31A-2047-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.769, 0.404, -0.495), (-0.639, 0.474, -0.605), (-0.01, 0.782, 0.623)
Vector: 38.135, -27.456, 36.293)

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Components

#1: Protein TRYPAREDOXIN II


Mass: 16928.457 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-165
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT STARTS AT RESIDUE 16

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.4 Msodium citrate1reservoir
2100 mMsodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / 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: 2.35→40 Å / Num. obs: 28025 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 29.8
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 9.6 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 40 Å / Num. obs: 35567 / % possible obs: 100 % / Num. measured all: 531442 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.76 Å / % possible obs: 100 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 9.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: OTHER / Resolution: 2.35→30 Å / SU B: 6.529 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.157 / Details: CNS USED IN INITIAL STAGES
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1414 5.1 %RANDOM
Rwork0.20083 ---
obs0.20155 26560 97.5 %-
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å20 Å2
2---2.08 Å20 Å2
3---4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 0 110 2453
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.351 Å / Lowest resolution: 2.412 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.256 / Num. reflection Rwork: 126 / Total num. of bins used: 20

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