+Open data
-Basic information
Entry | Database: PDB / ID: 3tpk | ||||||
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Title | Crystal structure of the oligomer-specific KW1 antibody fragment | ||||||
Components | Immunoglobulin heavy chain antibody variable domain KW1 | ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin Heavy Chain Domains / VHH / Complementarity Determining Regions / CDR / oligomer-specific / Alzheimer's disease / Amyloid | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / BENZAMIDINE Function and homology information | ||||||
Biological species | Camelidae (mammal) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Parthier, C. / Morgado, I. / Stubbs, M.T. / Fandrich, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Molecular basis of beta-amyloid oligomer recognition with a conformational antibody fragment. Authors: Morgado, I. / Wieligmann, K. / Bereza, M. / Ronicke, R. / Meinhardt, K. / Annamalai, K. / Baumann, M. / Wacker, J. / Hortschansky, P. / Malesevic, M. / Parthier, C. / Mawrin, C. / Schiene- ...Authors: Morgado, I. / Wieligmann, K. / Bereza, M. / Ronicke, R. / Meinhardt, K. / Annamalai, K. / Baumann, M. / Wacker, J. / Hortschansky, P. / Malesevic, M. / Parthier, C. / Mawrin, C. / Schiene-Fischer, C. / Reymann, K.G. / Stubbs, M.T. / Balbach, J. / Gorlach, M. / Horn, U. / Fandrich, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tpk.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tpk.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 3tpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/3tpk ftp://data.pdbj.org/pub/pdb/validation_reports/tp/3tpk | HTTPS FTP |
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-Related structure data
Related structure data | 3ln9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 15102.599 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein was selected by phage display from a fully synthetic library that was partly based on naturally occurring sequences from Camelidae Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-BEN / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.16 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 200 mM Magnesium Formate, 20%(w/v)PEG 3350, Additive: Benzamidine Hydrochloride 1M , pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.21→30 Å / Num. all: 35385 / Num. obs: 31606 / % possible obs: 89.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 16.062 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 19.86 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 30.42 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3LN9 Resolution: 1.3→25.87 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1707 / WRfactor Rwork: 0.1412 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9174 / SU B: 1.292 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0476 / SU Rfree: 0.0472 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.19 Å2 / Biso mean: 15.3404 Å2 / Biso min: 6.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→25.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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