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Yorodumi- PDB-2dqt: High resolution crystal structure of the complex of the hydrolyti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dqt | |||||||||
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Title | High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog | |||||||||
Components | (IMMUNOGLOBULIN 6D9) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB / IMMUNOGLOBULIN | |||||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Kristensen, O. / Vassylyev, D.G. / Tanaka, F. / Ito, N. / Morikawa, K. / Fujii, I. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis Authors: Oda, M. / Ito, N. / Tsumuraya, T. / Suzuki, K. / Sakakura, M. / Fujii, I. #1: Journal: J.Mol.Biol. / Year: 1997 Title: Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: evidence for an essential histidine involved in transition state stabilization Authors: Miyashita, H. / Hara, T. / Tanimura, R. / Fukuyama, S. / Cagnon, C. / Kohara, A. / Fujii, I. #2: Journal: J.Am.Chem.Soc. / Year: 1995 Title: Correlation between Antigen-Combining-Site Structures and Functions within a Panel of Catalytic Antibodies Generated against a Single Transition State Analog Authors: Fujii, I. / Tanaka, F. / Miyashita, H. / Tanimura, R. / Kinoshita, K. #3: Journal: Protein Pept.Lett. / Year: 1995 Title: Crystallization and Preliminary X-Ray Analysis: Transition State Complex of a Chloramphenicol Prodrug Activation Specific Catalytic Antibody Authors: Kristensen, O. / Miyashita, H. / Vassylyev, D.G. / Tanaka, F. / Fujii, I. / Morikawa, K. #4: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1994 Title: A common ancestry for multiple catalytic antibodies generated against a single transition-state analog Authors: Miyashita, H. / Hara, T. / Tanimura, R. / Tanaka, F. / Kikuchi, M. / Fujii, I. #5: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1994 Title: A common ancestry for multiple catalytic antibodies generated against a single transition-state analog Authors: Miyashita, H. / Hara, T. / Tamimura, R. / Tanaka, F. / Kikuchi, M. / Fujii, I. #6: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1993 Title: Prodrug activation via catalytic antibodies Authors: Miyashita, H. / Karaki, Y. / Kikuchi, M. / Fujii, I. #7: Journal: To be Published Title: Thermodynamic and Structural Analyses of Hydrolytic Mechanism by Catalytic Antibodies Authors: Oda, M. / Ito, N. / Tsumuraya, T. / Suzuki, K. / Fujii, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dqt.cif.gz | 104.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dqt.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dqt ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dqt | HTTPS FTP |
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-Related structure data
Related structure data | 2dquC 2dtmC 2igfS C: citing same article (ref.) 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: 24101.729 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 6D9 MURINE-MURINE HYBRIDOMA / Secretion: ASCITES FLUID / References: UniProt: A2NHM3*PLUS |
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#2: Antibody | Mass: 24134.154 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 6D9 MURINE-MURINE HYBRIDOMA / Secretion: ASCITES FLUID / References: UniProt: P18527*PLUS |
#3: Chemical | ChemComp-CPD / [ |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % Description: THE MAIN DATA WAS COLLECTED USING THE WEISSENBERG METHOD, AND MERGED WITH DATA COLLECTED ON A DIP100 DETECTOR AT A WAVELENGTH OF 1.5418 A. |
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Crystal grow | pH: 8.3 Details: THE PRE-FORMED COMPLEX WAS CRYSTALLIZED FROM 17% PEG 4000, 50MM TRIS, 0.1MM EDTA, PH 8.3 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 1, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→6 Å / Num. obs: 28513 / % possible obs: 69 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 4.5 Å2 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 1.8→2 Å / % possible all: 44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IGF Resolution: 1.8→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 633464.55 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 88.9272 Å2 / ksol: 0.62315 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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