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Yorodumi- PDB-6x9x: Crystal structure of Fab fragment of Anti-HCV E2 antibody (HC84.26) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x9x | ||||||
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Title | Crystal structure of Fab fragment of Anti-HCV E2 antibody (HC84.26) | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / IMMUNE SYSTEM / anti HCV E2 / Fab fragment | ||||||
Function / homology | ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shahid, S. / Mariuzza, R.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Crystal Structure of a Bivalent Antibody Fab Fragment. Authors: Shahid, S. / Gao, M. / Travis Gallagher, D. / Pozharski, E. / Brinson, R.G. / Keck, Z.Y. / Foung, S.K.H. / Fuerst, T.R. / 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 | 6x9x.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x9x.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 6x9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x9x_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6x9x_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6x9x_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6x9x_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/6x9x ftp://data.pdbj.org/pub/pdb/validation_reports/x9/6x9x | HTTPS FTP |
-Related structure data
Related structure data | 5esaS 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 24962.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 expi / Production host: Homo sapiens (human) | ||||
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#2: Antibody | Mass: 23010.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 expi / Production host: Homo sapiens (human) | ||||
#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.4 M Ammonium Acetate, 20% PEG 2000 MME, Cryoprotectant-Ethylene glycol |
-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: Jun 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 53599 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Net I/σ(I): 26.41 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 5293 / CC1/2: 0.771 / CC star: 0.933 / Rpim(I) all: 0.326 / Rrim(I) all: 0.728 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ESA Resolution: 1.8→34.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.544 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.292 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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