[English] 日本語
Yorodumi- PDB-2ybr: Crystal structure of the human derived single chain antibody frag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ybr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/TOXIN / IMMUNE SYSTEM-TOXIN COMPLEX / SCORPION TOXIN | ||||||
Function / homology | Function and homology information sodium channel inhibitor activity / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) CENTRUROIDES NOXIUS HOFFMANN (Mexican scorpion) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Canul-Tec, J.C. / Riano-Umbarila, L. / Rudino-Pinera, E. / Becerril, B. / Possani, L.D. / Torres-Larios, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides Noxius Hoffmann by a Human-Derived Single Chain Antibody Fragment Authors: Canul-Tec, J.C. / Riano-Umbarila, L. / Rudino-Pinera, E. / Becerril, B. / Possani, L.D. / Torres-Larios, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ybr.cif.gz | 181.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ybr.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ybr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/2ybr ftp://data.pdbj.org/pub/pdb/validation_reports/yb/2ybr | HTTPS FTP |
---|
-Related structure data
Related structure data | 2yc1C 1cn2S 1dfbS 1qlrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Antibody | Mass: 12533.847 Da / Num. of mol.: 3 / Fragment: HEAVY CHAIN, RESIDUES 1-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSYN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1 #2: Antibody | Mass: 15418.860 Da / Num. of mol.: 3 / Fragment: LIGHT CHAIN, RESIDUES 118-263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSYN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1 #3: Protein | Mass: 7607.728 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) CENTRUROIDES NOXIUS HOFFMANN (Mexican scorpion) References: UniProt: P01495 #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 53 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: 100 MM BIS-TRIS, PH 5.5, 25% PEG 3350 AND 200 MM (NH4)2SO4. |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Nov 6, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→46.2 Å / Num. obs: 37179 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HOMOLOGY MODEL BASED ON PDB ENTRIES 1CN2, 1QLR, AND 1DFB Resolution: 2.55→45.72 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.478 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.766 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→45.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|