+Open data
-Basic information
Entry | Database: PDB / ID: 6rco | ||||||
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Title | PfRH5-binding monoclonal antibody R5.004 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Plasmodium falciparum Erythrocyte invasion Neutralisation Human monoclonal antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Alanine, D.G.W. / Draper, S.J. / Higgins, M.K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell / Year: 2019 Title: Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies. Authors: Alanine, D.G.W. / Quinkert, D. / Kumarasingha, R. / Mehmood, S. / Donnellan, F.R. / Minkah, N.K. / Dadonaite, B. / Diouf, A. / Galaway, F. / Silk, S.E. / Jamwal, A. / Marshall, J.M. / Miura, ...Authors: Alanine, D.G.W. / Quinkert, D. / Kumarasingha, R. / Mehmood, S. / Donnellan, F.R. / Minkah, N.K. / Dadonaite, B. / Diouf, A. / Galaway, F. / Silk, S.E. / Jamwal, A. / Marshall, J.M. / Miura, K. / Foquet, L. / Elias, S.C. / Labbe, G.M. / Douglas, A.D. / Jin, J. / Payne, R.O. / Illingworth, J.J. / Pattinson, D.J. / Pulido, D. / Williams, B.G. / de Jongh, W.A. / Wright, G.J. / Kappe, S.H.I. / Robinson, C.V. / Long, C.A. / Crabb, B.S. / Gilson, P.R. / Higgins, M.K. / Draper, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rco.cif.gz | 343.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rco.ent.gz | 290.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rco_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 6rco_full_validation.pdf.gz | 472.8 KB | Display | |
Data in XML | 6rco_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 6rco_validation.cif.gz | 57.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/6rco ftp://data.pdbj.org/pub/pdb/validation_reports/rc/6rco | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24651.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23053.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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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: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M lithium sulfate, 0.1 M NaAc pH 4.5, 30% PEG 8000 0.33% hexamminecobalt(III) chloride, 0.06 M MES monohydrate, 0.06 PIPES, 0.02 M HEPES chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→42.45 Å / Num. obs: 111530 / % possible obs: 95.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.53 Å2 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.66→1.69 Å / Num. unique obs: 5493 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→42.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.087
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Displacement parameters | Biso mean: 45.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.66→42.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.7 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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