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Yorodumi- PDB-1h8n: Three-dimensional structure of anti-ampicillin single chain Fv fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h8n | ||||||
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Title | Three-dimensional structure of anti-ampicillin single chain Fv fragment from phage-displayed murine antibody libraries | ||||||
Components | MUTANT AL2 6E7S9G | ||||||
Keywords | ANTIBODY / FRAMEWORK | ||||||
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: 1.87 Å | ||||||
Authors | Jung, S. / Spinelli, S. / Schimmele, B. / Honegger, A. / Pugliese, L. / Cambillau, C. / Pluckthun, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The Importance of Framework Residues H6, H7 and H10 in Antibody Heavy Chains: Experimental Evidence for a New Structural Subclassification of Antibody V(H) Domains Authors: Jung, S. / Spinelli, S. / Schimmele, B. / Honegger, A. / Pugliese, L. / Cambillau, C. / Pluckthun, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h8n.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8n.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h8n_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 1h8n_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 1h8n_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 1h8n_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8n ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8n | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 26996.697 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT Source method: isolated from a genetically manipulated source Details: SINGLE CHAIN FV ANTIBODY IN WHICH THE VL AND VH FRAGMENTS ARE JOINED BY A GGGGSGGGGSGGGGSGGGGS LINKER Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 5.8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9882 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9882 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 20522 / % possible obs: 98.8 % / Redundancy: 3 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.08 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.245 / % possible all: 80 |
Reflection | *PLUS Num. measured all: 303033 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.275 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1715751.43 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.9106 Å2 / ksol: 0.405662 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.87→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.99 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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