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Yorodumi- PDB-7sx6: Crystal structure of broadly neutralizing antibody N49P9.3 Fab in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sx6 | ||||||||||||
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Title | Crystal structure of broadly neutralizing antibody N49P9.3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 / VRC01-CLASS ANTIBODY / CD4 BINDING SITE / CLADE A/E 93TH057 GP120 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / N49P9.3 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / clade A/E 93TH057 HIV-1 gp120 core Function and homology information | ||||||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||||||||
Authors | Tolbert, W.D. / Pazgier, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Crystal structure of broadly neutralizing antibody N49P9.3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core Authors: Tolbert, W.D. / Pazgier, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sx6.cif.gz | 622.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sx6.ent.gz | 519.3 KB | Display | PDB format |
PDBx/mmJSON format | 7sx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sx6_validation.pdf.gz | 518.7 KB | Display | wwPDB validaton report |
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Full document | 7sx6_full_validation.pdf.gz | 570.7 KB | Display | |
Data in XML | 7sx6_validation.xml.gz | 58.2 KB | Display | |
Data in CIF | 7sx6_validation.cif.gz | 77.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/7sx6 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/7sx6 | HTTPS FTP |
-Related structure data
Related structure data | 6oz3S S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules HBLC
#2: Antibody | Mass: 24321.479 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 21763.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human) |
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-Protein / Sugars , 2 types, 22 molecules GA
#1: Protein | Mass: 39356.613 Da / Num. of mol.: 2 / Mutation: H375S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9 #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 5 molecules
#5: Chemical | #6: Chemical | |
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-Details
Has ligand of interest | N |
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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: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 4000 0.1 M HEPES pH 7.5 0.1 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 25011 / % possible obs: 97.6 % / Redundancy: 3.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.074 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 3.4→3.46 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1163 / CC1/2: 0.513 / Rpim(I) all: 0.725 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OZ3 Resolution: 3.4→35.46 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 35.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→35.46 Å
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Refine LS restraints |
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LS refinement shell |
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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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