+Open data
-Basic information
Entry | Database: PDB / ID: 8awl | ||||||||||||
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Title | Fab RVFV-268 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab fragment antibody | ||||||||||||
Function / homology | CITRIC ACID Function and homology information | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å | ||||||||||||
Authors | Hulswit, R.J.G. / Bowden, T.A. / Stass, R. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Multifunctional human monoclonal antibody combination mediates protection against Rift Valley fever virus at low doses. Authors: Chapman, N.S. / Hulswit, R.J.G. / Westover, J.L.B. / Stass, R. / Paesen, G.C. / Binshtein, E. / Reidy, J.X. / Engdahl, T.B. / Handal, L.S. / Flores, A. / Gowen, B.B. / Bowden, T.A. / Crowe Jr., J.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8awl.cif.gz | 181.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8awl.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 8awl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8awl_validation.pdf.gz | 797 KB | Display | wwPDB validaton report |
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Full document | 8awl_full_validation.pdf.gz | 798.8 KB | Display | |
Data in XML | 8awl_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 8awl_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/8awl ftp://data.pdbj.org/pub/pdb/validation_reports/aw/8awl | HTTPS FTP |
-Related structure data
Related structure data | 8awmC 5zmjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23633.486 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: 22768.014 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-CIT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M citric acid pH 3.5, 20% w/v polyethylene glycol (PEG) 1,500 and 4% v/v (+/-)-2-methyl-2,4-pentanediol Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→47.74 Å / Num. obs: 64027 / % possible obs: 99.5 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.62→1.65 Å / Num. unique obs: 3003 / CC1/2: 0.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZMJ Resolution: 1.62→47.74 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.07 Å2 / Biso mean: 33.4045 Å2 / Biso min: 19.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.62→47.74 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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Refinement TLS params. | Method: refined / Origin x: -42.9439 Å / Origin y: -24.517 Å / Origin z: 16.5363 Å
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Refinement TLS group |
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