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Yorodumi- PDB-6w16: Crystal structure of a human metapneumovirus monomeric fusion pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w16 | |||||||||
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Title | Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458 Fab | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / F protein | |||||||||
Function / homology | Function and homology information membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Human metapneumovirus Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Huang, J. / Mousa, J.J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Plos Pathog. / Year: 2020 Title: Antibody recognition of the Pneumovirus fusion protein trimer interface. Authors: Huang, J. / Diaz, D. / Mousa, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w16.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w16.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 6w16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w16_validation.pdf.gz | 914.8 KB | Display | wwPDB validaton report |
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Full document | 6w16_full_validation.pdf.gz | 926.9 KB | Display | |
Data in XML | 6w16_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 6w16_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/6w16 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/6w16 | HTTPS FTP |
-Related structure data
Related structure data | 5wb0S S: Starting model for refinement |
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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: Protein | Mass: 59099.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human metapneumovirus, (gene. exp.) Human immunodeficiency virus 1 Production host: Homo sapiens (human) / References: UniProt: Q6W8S4, UniProt: M1E1E4 |
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#2: Antibody | Mass: 23316.221 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: Antibody | Mass: 23586.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#5: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→47.9 Å / Num. obs: 31997 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1407 / Rpim(I) all: 0.03155 / Rrim(I) all: 0.1443 / Net I/σ(I): 17.62 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 20.9 % / Num. unique obs: 4679 / CC1/2: 0.621 / CC star: 0.875 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WB0 Resolution: 3.1→41.05 Å / SU ML: 0.4638 / Cross valid method: FREE R-VALUE / Phase error: 26.639
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→41.05 Å
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Refine LS restraints |
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LS refinement shell |
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