+Open data
-Basic information
Entry | Database: PDB / ID: 5esa | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of anti-HCV E2 antibody HC84-26 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Hepatitis C virus / E2 glycoprotein / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Gao, M. / Mariuzza, R. | ||||||
Citation | Journal: To be Published Title: Crystal structure of anti-HCV E2 antibody HC84-26 Authors: Gao, M. / Mariuzza, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5esa.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5esa.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 5esa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5esa_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5esa_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 5esa_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 5esa_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/5esa ftp://data.pdbj.org/pub/pdb/validation_reports/es/5esa | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23087.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) |
---|---|
#2: Antibody | Mass: 23381.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% w/v PEG1000, 0.1 M sodium cacodylate/HCl, pH 6.5, 0.2 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→37.17 Å / Num. obs: 12733 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.6→2.693 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 6.6 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37.17 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.81 Å2 / Biso mean: 27.8809 Å2 / Biso min: 8.53 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→37.17 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %
|