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Yorodumi- PDB-8tfe: Crystal structure of Fab fragment of anti-HCV E2 antibody (CBH-7) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tfe | ||||||
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Title | Crystal structure of Fab fragment of anti-HCV E2 antibody (CBH-7) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / E2 glycoprotein / Fab fragment | ||||||
Function / homology | CITRATE ANION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Shahid, S. / Mariuzza, R.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Fab fragment of anti-HCV E2 antibody (CBH-7) Authors: Shahid, S. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tfe.cif.gz | 321.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tfe.ent.gz | 263.7 KB | Display | PDB format |
PDBx/mmJSON format | 8tfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tfe_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8tfe_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8tfe_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 8tfe_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/8tfe ftp://data.pdbj.org/pub/pdb/validation_reports/tf/8tfe | HTTPS FTP |
-Related structure data
Related structure data | 6x9xS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 27417.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 25477.658 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-FLC / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1M Sodium phosphate dibasic pH 4.2, 0.2 M NaCl, and 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 107383 / % possible obs: 98.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.42 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Net I/σ(I): 27.75 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.544 / Num. unique obs: 5314 / CC1/2: 0.911 / CC star: 0.976 / Rpim(I) all: 0.238 / Rrim(I) all: 0.595 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6X9X Resolution: 1.62→46.14 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.222 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 23.222 Å2
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Refinement step | Cycle: 1 / Resolution: 1.62→46.14 Å
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Refine LS restraints |
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