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- PDB-1tqc: Ovine recombinant PrP(114-234), ARR variant in complex with the V... -

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Basic information

Entry
Database: PDB / ID: 1tqc
TitleOvine recombinant PrP(114-234), ARR variant in complex with the VRQ14 Fab fragment (IgG2a)
Components
  • VRQ14 Fab Heavy chain
  • VRQ14 Fab light chain
  • prion proteinPRNP
KeywordsUNKNOWN FUNCTION/IMMUNE SYSTEM / prion / antibody / UNKNOWN FUNCTION-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


side of membrane / tubulin binding / protein homooligomerization / microtubule binding / copper ion binding / Golgi apparatus / identical protein binding / plasma membrane
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily ...Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesOvis aries (sheep)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEghiaian, F. / Grosclaude, J. / Lesceu, S. / Debey, P. / Doublet, B. / Treguer, E. / Rezaei, H. / Knossow, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Insight into the PrPC-->PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants
Authors: Eghiaian, F. / Grosclaude, J. / Lesceu, S. / Debey, P. / Doublet, B. / Treguer, E. / Rezaei, H. / Knossow, M.
History
DepositionJun 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prion protein
B: VRQ14 Fab Heavy chain
C: VRQ14 Fab light chain


Theoretical massNumber of molelcules
Total (without water)59,1643
Polymers59,1643
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.659, 145.448, 43.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein prion protein / PRNP / OvPrP


Mass: 12197.569 Da / Num. of mol.: 1 / Fragment: ARR variant, residues 127-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: PRNP sheep ARR variant / Plasmid: pET28-a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P23907
#2: Antibody VRQ14 Fab Heavy chain


Mass: 22810.455 Da / Num. of mol.: 1 / Fragment: VRQ14 Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody VRQ14 Fab light chain


Mass: 24155.863 Da / Num. of mol.: 1 / Fragment: VRQ14 Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Sodium citrate 0.1M , PEG8000, Ammonium acetate 0.2M, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97926 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 15206 / Num. obs: 15206 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.1
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→14.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1402432.59 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1507 10.2 %RANDOM
Rwork0.222 ---
all0.23 ---
obs0.222 14820 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.5963 Å2 / ksol: 0.344842 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1--15.21 Å20 Å20 Å2
2---21.3 Å20 Å2
3---36.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.36 Å
Luzzati d res low-15 Å
Luzzati sigma a0.43 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4159 0 0 22 4181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 221 9.1 %
Rwork0.311 2203 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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