+Open data
-Basic information
Entry | Database: PDB / ID: 5jrp | ||||||
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Title | crystal structure of monoclonal antibody MR78 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Marberg Virus / monoclonal 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 / Resolution: 2 Å | ||||||
Authors | Dong, J. / Crowe, J. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Role of Non-local Interactions between CDR Loops in Binding Affinity of MR78 Antibody to Marburg Virus Glycoprotein. Authors: Sangha, A.K. / Dong, J. / Williamson, L. / Hashiguchi, T. / Saphire, E.O. / Crowe, J.E. / Meiler, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jrp.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jrp.ent.gz | 158.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jrp_validation.pdf.gz | 419.8 KB | Display | wwPDB validaton report |
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Full document | 5jrp_full_validation.pdf.gz | 420.5 KB | Display | |
Data in XML | 5jrp_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 5jrp_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/5jrp ftp://data.pdbj.org/pub/pdb/validation_reports/jr/5jrp | HTTPS FTP |
-Related structure data
Related structure data | 5weqC 3x2d 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 23364.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23869.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-NA / |
#4: 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: 3.88 Å3/Da / Density % sol: 68.28 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / Details: 4.5 M NaCl, 0.1 M Tris-HCl, pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 49786 / % possible obs: 100 % / Redundancy: 11.2 % / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.439 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X2D 3x2d Resolution: 2→50 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 43.4012 Å / Origin y: -29.7811 Å / Origin z: -32.604 Å
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Refinement TLS group | Selection details: all |