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Yorodumi- PDB-4hha: Anti-Human Cytomegalovirus (HCMV) Fab KE5 with epitope peptide AD-2S1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hha | ||||||
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Title | Anti-Human Cytomegalovirus (HCMV) Fab KE5 with epitope peptide AD-2S1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab fragment / Antibody | ||||||
Function / homology | Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Glycoprotein B Function and homology information | ||||||
Biological species | Homo sapiens (human) Human herpesvirus 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Bryson, S. / Risnes, L. / Damgupta, S. / Thomson, C.A. / Pfoh, R. / Schrader, J.W. / Pai, E.F. | ||||||
Citation | Journal: J. Immunol. / Year: 2016 Title: Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation. Authors: Bryson, S. / Thomson, C.A. / Risnes, L.F. / Dasgupta, S. / Smith, K. / Schrader, J.W. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hha.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hha.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/4hha ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hha | HTTPS FTP |
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-Related structure data
Related structure data | 4hh9SC 4hieC 4hihC 4hiiC 4hijC 4pttC 4ptuC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Antibody | Mass: 23471.064 Da / Num. of mol.: 1 / Fragment: Fab fragment KE5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) | ||
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#2: Antibody | Mass: 25400.516 Da / Num. of mol.: 1 / Fragment: AD-2S1 eptiope / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) | ||
#3: Protein/peptide | Mass: 1246.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Human herpesvirus 5 / References: UniProt: Q9YKI2 | ||
#4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.05M Na Acetate, pH 4.2, 18% Jeffamine 1500, 0.2M Ammonium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 28, 2012 / Details: Toroidal focusing mirror |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→43 Å / Num. all: 49164 / Num. obs: 48944 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.72 % / Rmerge(I) obs: 0.0478 / Net I/σ(I): 19.84 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.89 / Num. unique all: 4260 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HH9 Resolution: 1.6→43 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→43 Å
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Refine LS restraints |
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