[English] 日本語
Yorodumi- PDB-8da0: Crystal structure of Mamba alpha-neurotoxin in complex with Centi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8da0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Mamba alpha-neurotoxin in complex with Centi-3FTX-D09 antibody | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / ANTITOXIN/TOXIN / antivenom / 3-finger toxin / alpha-neurotoxin / long neurotoxin 1 / antibody / ANTITOXIN / ANTITOXIN-TOXIN complex | |||||||||
Function / homology | Function and homology information acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Dendroaspis polylepis polylepis (black mamba) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Pletnev, S. / Verardi, R. / Tully, E.S. / Glanville, J. / Kwong, P.D. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: To Be Published Title: Venom protection by antibody from a snakebite hyperimmune subject Authors: Glanville, J. / Andrade, J. / Bellin, M. / Kim, S. / Pletnev, S. / Tsao, D. / Verardi, R. / Bedi, R. / Friede, T. / Tully, E. / Zhang, B. / Bylund, T. / Liu, T. / Kwong, P.D. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8da0.cif.gz | 210.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8da0.ent.gz | 167.4 KB | Display | PDB format |
PDBx/mmJSON format | 8da0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8da0 ftp://data.pdbj.org/pub/pdb/validation_reports/da/8da0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8d9yC 8d9zC 8da1C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules EF
#3: Protein | Mass: 8015.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dendroaspis polylepis polylepis (black mamba) Production host: Homo sapiens (human) / References: UniProt: C0HJD7 |
---|
-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 23339.740 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 25132.959 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
---|
-Non-polymers , 4 types, 572 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1M Tris pH 8.5, 10% PEG4000, 50mM Proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→30 Å / Num. obs: 50268 / % possible obs: 94.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.168 / Rrim(I) all: 0.296 / Χ2: 1.397 / Net I/σ(I): 5.6 / Num. measured all: 138319 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model found by BALBES software using input sequence Resolution: 2.2→29.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 8.079 / SU ML: 0.193 / SU R Cruickshank DPI: 0.3064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.95 Å2 / Biso mean: 23.638 Å2 / Biso min: 1.37 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→29.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.205→2.262 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|