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Yorodumi- PDB-1h8o: Three-dimensional structure of anti-ampicillin single chain Fv fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h8o | ||||||
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Title | Three-dimensional structure of anti-ampicillin single chain Fv fragment. | ||||||
Components | MUTANT AL2 6E7P9G | ||||||
Keywords | ANTIBODY / FV FRAGMENT / ANTI-AMPICILLIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 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 | 1h8o.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8o.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 1h8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8o ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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 | #3: 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: 49.05 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 5 | ||||||||||||||||||||||||||||||
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 / Wavelength: 1.54178 |
Detector | Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→12 Å / Num. obs: 14189 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rsym value: 0.11 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.4 / % possible all: 90.7 |
Reflection | *PLUS Num. measured all: 81293 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 90.7 % / Rmerge(I) obs: 0.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→11.94 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1342809.82 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.0488 Å2 / ksol: 0.31283 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→11.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.031 / 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: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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