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Yorodumi- PDB-5x5x: Crystal structure of the Fab fragment of anti-osteocalcin C-termi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x5x | ||||||||||||||||||||||||
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Title | Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219 | ||||||||||||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Quenchbody (Q-body) / Immunoglobulin fold / Osteocalcin / Open Sandwich Immunoassay (OS-IA) | ||||||||||||||||||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / FORMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL Function and homology information | ||||||||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||||||||||||||||||||
Authors | Komatsu, M. / Dong, J. / Ueda, H. / Arai, R. | ||||||||||||||||||||||||
Funding support | Japan, 7items
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Citation | Journal: To be published Title: Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219 Authors: Arai, R. / Komatsu, M. / Dong, J. / Ueda, H. #1: Journal: Anal. Chem. / Year: 2007 Title: Noncompetitive detection of low molecular weight peptides by open sandwich immunoassay. Authors: Lim, S.L. / Ichinose, H. / Shinoda, T. / Ueda, H. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x5x.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x5x.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 5x5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/5x5x ftp://data.pdbj.org/pub/pdb/validation_reports/x5/5x5x | HTTPS FTP |
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-Related structure data
Related structure data | 4kuzS 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 on special symmetry positions |
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-Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 26202.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma KTM-219 / Plasmid: pET-Fab / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY |
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#2: Antibody | Mass: 25259.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma KTM-219 / Plasmid: pET-Fab / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY |
-Non-polymers , 5 types, 250 molecules
#3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.6 M sodium formate, 29% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 35733 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.3 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Rsym value: 0.066 / Χ2: 1.015 / Net I/av σ(I): 26.6 / Net I/σ(I): 12.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | 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: 4KUZ Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.128 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1516 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.142 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.85 Å2 / Biso mean: 31.038 Å2 / Biso min: 13.37 Å2
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Refinement step | Cycle: final / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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