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Yorodumi- PDB-1dlf: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI... -
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-Basic information
Entry | Database: PDB / ID: 1dlf | ||||||
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Title | HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25 | ||||||
Components | (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)) x 2 | ||||||
Keywords | IMMUNOGLOBULIN / FV FRAGMENT | ||||||
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 / MULTIPLE MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Nakasako, M. / Takahashi, H. / Shimada, I. / Arata, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody. Authors: Nakasako, M. / Takahashi, H. / Shimba, N. / Shimada, I. / Arata, Y. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Role of the Domain-Domain Interaction in the Construction of the Antigen Combining Site. A Comparative Study by 1H-15N Shift Correlation NMR Spectroscopy of the Fv and Fab Fragments of Anti- ...Title: Role of the Domain-Domain Interaction in the Construction of the Antigen Combining Site. A Comparative Study by 1H-15N Shift Correlation NMR Spectroscopy of the Fv and Fab Fragments of Anti-Dansyl Mouse Monoclonal Antibody Authors: Takahashi, H. / Tamura, H. / Shimba, N. / Shimada, I. / Arata, Y. #2: Journal: Biochemistry / Year: 1992 Title: Dynamical Structure of the Antibody Combining Site as Studied by 1H-15N Shift Correlation NMR Spectroscopy Authors: Takahashi, H. / Suzuki, E. / Shimada, I. / Arata, Y. #3: Journal: Biochemistry / Year: 1992 Title: Isotope-Edited Nuclear Magnetic Resonance Study of Fv Fragment of Anti-Dansyl Mouse Monoclonal Antibody: Recognition of the Dansyl Hapten Authors: Odaka, A. / Kim, J.I. / Takahashi, H. / Shimada, I. / Arata, Y. #4: Journal: Biochemistry / Year: 1991 Title: Preparation of the Fv Fragment from a Short-Chain Mouse Igg2A Anti-Dansyl Monoclonal Antibody and Use of Selectively Deuterated Fv Analogues for Two-Dimensional 1H NMR Analyses of the Antigen-Antibody Interactions Authors: Takahashi, H. / Igarashi, T. / Shimada, I. / Arata, Y. #5: Journal: Biochemistry / Year: 1991 Title: Multinuclear NMR Study of the Structure of the Fv Fragment of Anti-Dansyl Mouse Igg2A Antibody Authors: Takahashi, H. / Odaka, A. / Kawaminami, S. / Matsunaga, C. / Kato, K. / Shimada, I. / Arata, Y. #6: Journal: J.Am.Chem.Soc. / Year: 1991 Title: Conformation and Stereoselective Reduction of Hapten Side Chain in the Antibody Combining Site Authors: Kim, T. / Nakano, I. / Higuchi, T. / Hirobe, M. / Shimada, I. / Arata, Y. #7: Journal: Biochemistry / Year: 1990 Title: Structure of a Mouse Immunoglobulin G that Lacks the Entire Ch1 Domain: Protein Sequencing and Small-Angle X-Ray Scattering Studies Authors: Igarashi, T. / Sato, M. / Katsube, Y. / Takio, K. / Tanaka, T. / Nakanishi, M. / Arata, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dlf.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dlf.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/1dlf ftp://data.pdbj.org/pub/pdb/validation_reports/dl/1dlf | HTTPS FTP |
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-Related structure data
Related structure data | 2dlfC 1igfS S: Starting model for refinement C: citing same article (ref.) |
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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 / Fragment: FV FRAGMENT (VH AND VL DOMAINS) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / References: UniProt: Q9JL82, UniProt: P01631*PLUS | ||||
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#2: Antibody | Mass: 14152.787 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT (VH AND VL DOMAINS) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / References: PIR: PC1213 | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | THE ANTI-DANSYL FV FRAGMENT RETAINS ITS FULL ANTIGEN BINDING CAPABILITY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 39.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.25 / Details: pH 5.25 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 112 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 8, 1998 Details: DOUBLE FOCUSSING MIRROR (PT COATED AND NI COATED MIRRORS) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→99 Å / Num. obs: 36158 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 8.3 / Rsym value: 0.265 / % possible all: 94.4 |
Reflection | *PLUS Num. measured all: 280945 |
-Processing
Software |
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Refinement | Method to determine structure: MULTIPLE MOLECULAR REPLACEMENT Starting model: FV PORTION OF FAB' B13I2 (1IGF) Resolution: 1.45→8 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 1 / Isotropic thermal model: GAUSS / σ(F): 2 / Details: ALL ATOMS IN AN ASYMMETRIC UNIT WERE REFINED
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.46 Å / Total num. of bins used: 40
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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