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Yorodumi- PDB-1h8s: Three-dimensional structure of anti-ampicillin single chain Fv fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h8s | ||||||
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Title | Three-dimensional structure of anti-ampicillin single chain Fv fragment complexed with the hapten. | ||||||
Components | MUTANT AL2 6E7P9G | ||||||
Keywords | ANTI-AMPICILLIN ANTIBODIES | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-AIC Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å | ||||||
Authors | Burmester, J. / Spinelli, S. / Pugliese, L. / Krebber, A. / Honegger, A. / Jung, S. / Schimmele, B. / Cambillau, C. / Pluckthun, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Selection, Characterization and X-Ray Structure of Anti-Ampicillin Single-Chain Fv Fragments from Phage-Displayed Murine Antibody Libraries Authors: Burmester, J. / Spinelli, S. / Pugliese, L. / Krebber, A. / Honegger, A. / Jung, S. / Schimmele, B. / 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 | 1h8s.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8s.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h8s_validation.pdf.gz | 762.5 KB | Display | wwPDB validaton report |
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Full document | 1h8s_full_validation.pdf.gz | 774.1 KB | Display | |
Data in XML | 1h8s_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 1h8s_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8s ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 27006.734 Da / Num. of mol.: 2 / 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) / Plasmid: PAK3000 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): RV308 #2: Chemical | ChemComp-AIC / ( | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 46.49 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.00 | ||||||||||||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→13 Å / Num. obs: 20445 / % possible obs: 98 % / Redundancy: 3 % / Biso Wilson estimate: 38.8 Å2 / Rsym value: 0.082 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.2 / % possible all: 92 |
Reflection | *PLUS % possible obs: 98 % / Num. measured all: 93952 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 82.8 % / Rmerge(I) obs: 0.225 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.4→12.94 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.6877 Å2 / ksol: 0.335775 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→12.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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