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Yorodumi- PDB-2z92: Crystal structure of the Fab fragment of anti-ciguatoxin antibody... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z92 | ||||||
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Title | Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C_ABCDE | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobrin fold | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRIC ACID / Chem-ENE Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ui, M. / Tanaka, Y. / Tsumoto, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9 Authors: Ui, M. / Tanaka, Y. / Tsumuraya, T. / Fujii, I. / Inoue, M. / Hirama, M. / Tsumoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z92.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z92.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 2z92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/2z92 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/2z92 | HTTPS FTP |
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-Related structure data
Related structure data | 2z91C 2z93C 1hq4S 1yecS 1z3gS 3f58S 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: 23837.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma |
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#2: Antibody | Mass: 23223.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma |
#3: Chemical | ChemComp-ENE / ( |
#4: Chemical | ChemComp-CIT / |
#5: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE HAS BEEN ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE HAS BEEN DEPOSITED IN THE SEQUENCE DATABASE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M tri-sodium Citrate dihydrate, 20% iso-Propanol, 20% PEG4000, pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 21987 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.103 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.7 % / Num. unique all: 2102 / Rsym value: 0.337 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HQ4, 1Z3G, 3F58, 1YEC Resolution: 2.3→9.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 55317.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.1537 Å2 / ksol: 0.486365 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→9.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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