+Open data
-Basic information
Entry | Database: PDB / ID: 5ayu | ||||||
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Title | Crystal structure of HyHEL-10 Fv | ||||||
Components |
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Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Nakanishi, T. / Tsumoto, K. / Yokota, A. / Kondo, H. / Kumagai, I. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of HyHEL-10 Fv Authors: Nakanishi, T. / Tsumoto, K. / Yokota, A. / Kondo, H. / Kumagai, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ayu.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ayu.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ayu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5ayu ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ayu | HTTPS FTP |
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-Related structure data
Related structure data | 1c08S 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: 11623.810 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) | ||||
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#2: Antibody | Mass: 12724.862 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.28 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.2 Details: 0.1M Tris-HCl, 1.5M ammonium sulfate, 12% glycerol, pH 9.2 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 22939 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 11 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 9.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C08 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.509 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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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 mean: 22.11 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→20 Å
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Refine LS restraints |
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