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Yorodumi- PDB-5aaw: Structure of a redesigned cross-reactive antibody to dengue virus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aaw | |||||||||
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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 | VIRAL PROTEIN / 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: 3.27 Å | |||||||||
Authors | Wong, Y. / Robinson, L. / 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 | 5aaw.cif.gz | 378.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aaw.ent.gz | 310 KB | Display | PDB format |
PDBx/mmJSON format | 5aaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aaw_validation.pdf.gz | 508.6 KB | Display | wwPDB validaton report |
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Full document | 5aaw_full_validation.pdf.gz | 535.5 KB | Display | |
Data in XML | 5aaw_validation.xml.gz | 64.6 KB | Display | |
Data in CIF | 5aaw_validation.cif.gz | 88.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/5aaw ftp://data.pdbj.org/pub/pdb/validation_reports/aa/5aaw | HTTPS FTP |
-Related structure data
Related structure data | 5aamC 4ud3 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Antibody | Mass: 27427.488 Da / Num. of mol.: 6 / Fragment: SCFV 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.: 6 / Fragment: D3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DENGUE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6YFR6*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: 2.1 Å3/Da / Density % sol: 41.48 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 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: 3.27→105.53 Å / Num. obs: 31554 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 3.27→3.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.5 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UD3 4ud3 Resolution: 3.27→48.75 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.844 / SU B: 35.888 / SU ML: 0.547 / Cross valid method: THROUGHOUT / ESU R Free: 0.618 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.975 Å2
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Refinement step | Cycle: LAST / Resolution: 3.27→48.75 Å
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Refine LS restraints |
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