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Yorodumi- PDB-1wz1: Crystal structure of the Fv fragment complexed with dansyl-lysine -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wz1 | ||||||
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Title | Crystal structure of the Fv fragment complexed with dansyl-lysine | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antigen-antibody fragent complex | ||||||
Function / homology | Function and homology information immunoglobulin complex / antigen binding / adaptive immune response / immune response / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Nakasako, M. / Oka, T. / Mashumo, M. / Takahashi, H. / Shimada, I. / Yamaguchi, Y. / Kato, K. / Arata, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten Authors: Nakasako, M. / Oka, T. / Mashumo, M. / Takahashi, H. / Shimada, I. / Yamaguchi, Y. / Kato, K. / Arata, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wz1.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wz1.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wz1_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 1wz1_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 1wz1_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1wz1_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/1wz1 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/1wz1 | HTTPS FTP |
-Related structure data
Related structure data | 2dlfS 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: 12386.949 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) / References: GenBank: 1407754, UniProt: P01631*PLUS |
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#2: Antibody | Mass: 13995.593 Da / Num. of mol.: 1 / Fragment: Fv fragment(residues 1-123) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-DNS / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, magnecium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jan 1, 2004 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→81.6 Å / Num. obs: 23960 / % possible obs: 100 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.078 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.8→1.82 Å / Rmerge(I) obs: 0.421 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DLF Resolution: 1.85→81.6 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.85→81.6 Å
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Refine LS restraints |
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