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- PDB-2z92: Crystal structure of the Fab fragment of anti-ciguatoxin antibody... -
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Open data
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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 | ||||||
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![]() | IMMUNE SYSTEM / Immunoglobrin fold | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRIC ACID / Chem-ENE![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ui, M. / Tanaka, Y. / Tsumoto, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.6 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2z91C ![]() 2z93C ![]() 1hq4S ![]() 1yecS ![]() 1z3gS ![]() 3f58S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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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.) ![]() ![]() |
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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