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Yorodumi- PDB-5aam: Structure of a redesigned cross-reactive antibody to dengue virus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aam | |||||||||
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Title | Structure of a redesigned cross-reactive antibody to dengue virus with increased in vivo potency | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / SCFV DENGUE ANTIBODY ENVELOPE DOMAIN III | |||||||||
Function / homology | Function and homology information viral capsid / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / endoplasmic reticulum membrane / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) DENGUE VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | |||||||||
Authors | Wong, Y.H. / Robinson, L.N. / Lescar, J. / Sasisekharan, R. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2015 Title: Structure-Guided Design of an Anti-Dengue Antibody Directed to a Non-Immunodominant Epitope. Authors: Robinson, L.N. / Tharakaraman, K. / Rowley, K.J. / Costa, V.V. / Chan, K.R. / Wong, Y.H. / Ong, L.C. / Tan, H.C. / Koch, T. / Cain, D. / Kirloskar, R. / Viswanathan, K. / Liew, C.W. / ...Authors: Robinson, L.N. / Tharakaraman, K. / Rowley, K.J. / Costa, V.V. / Chan, K.R. / Wong, Y.H. / Ong, L.C. / Tan, H.C. / Koch, T. / Cain, D. / Kirloskar, R. / Viswanathan, K. / Liew, C.W. / Tissire, H. / Ramakrishnan, B. / Myette, J.R. / Babcock, G.J. / Sasisekharan, V. / Alonso, S. / Chen, J. / Lescar, J. / Shriver, Z. / Ooi, E.E. / Sasisekharan, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aam.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aam.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 5aam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aam_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 5aam_full_validation.pdf.gz | 469.4 KB | Display | |
Data in XML | 5aam_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 5aam_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/5aam ftp://data.pdbj.org/pub/pdb/validation_reports/aa/5aam | HTTPS FTP |
-Related structure data
Related structure data | 5aawC 3uypS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 27299.357 Da / Num. of mol.: 2 / Fragment: SCFV, RESIDUES 2-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) #2: Protein | Mass: 12692.560 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DENGUE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: U3N5N6, UniProt: Q6YFU0*PLUS #3: 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: 2.11 Å3/Da / Density % sol: 41.67 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 29, 2014 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→47.9 Å / Num. obs: 23183 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 80.51 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.49→2.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 1.4 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UYP Resolution: 2.49→29.55 Å / Cor.coef. Fo:Fc: 0.9426 / Cor.coef. Fo:Fc free: 0.9169 / SU R Cruickshank DPI: 0.766 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.738 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.317
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Displacement parameters | Biso mean: 85.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.428 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→29.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.6 Å / Total num. of bins used: 12
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