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Yorodumi- PDB-6utb: CRYSTAL STRUCTURE OF UNLIGANDED HIV-1 LM/HT CLADE A/E CRF01 GP120 CORE -
+Open data
-Basic information
Entry | Database: PDB / ID: 6utb | ||||||||||||
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Title | CRYSTAL STRUCTURE OF UNLIGANDED HIV-1 LM/HT CLADE A/E CRF01 GP120 CORE | ||||||||||||
Components | HIV-1 LM/HT Clade A/E CRF01 gp120 core | ||||||||||||
Keywords | IMMUNE SYSTEM / HIV-1 GP120 / CLADE A/E CF01 / VIRAL PROTEIN | ||||||||||||
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 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||||||||
Authors | Tolbert, W.D. / Sherburn, R. / Pazgier, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Mbio / Year: 2020 Title: The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site. Authors: Prevost, J. / Tolbert, W.D. / Medjahed, H. / Sherburn, R.T. / Madani, N. / Zoubchenok, D. / Gendron-Lepage, G. / Gaffney, A.E. / Grenier, M.C. / Kirk, S. / Vergara, N. / Han, C. / Mann, B.T. ...Authors: Prevost, J. / Tolbert, W.D. / Medjahed, H. / Sherburn, R.T. / Madani, N. / Zoubchenok, D. / Gendron-Lepage, G. / Gaffney, A.E. / Grenier, M.C. / Kirk, S. / Vergara, N. / Han, C. / Mann, B.T. / Chenine, A.L. / Ahmed, A. / Chaiken, I. / Kirchhoff, F. / Hahn, B.H. / Haim, H. / Abrams, C.F. / Smith 3rd, A.B. / Sodroski, J. / Pazgier, M. / Finzi, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6utb.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6utb.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 6utb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/6utb ftp://data.pdbj.org/pub/pdb/validation_reports/ut/6utb | HTTPS FTP |
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-Related structure data
Related structure data | 6uswC 6ut1C 6utdC 3tgtS 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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Unit cell |
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-Components
#1: Protein | Mass: 39466.750 Da / Num. of mol.: 1 / Mutation: H61Y, Q105H, V108I, H375T, N474D, I475M, K476R 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 | ||||||
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#2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | 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: 2.48 Å3/Da / Density % sol: 50.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 1500, 10% PEG 400, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92007 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2018 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92007 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 13726 / % possible obs: 96.7 % / Redundancy: 4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.165 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2025 / CC1/2: 0.7 / % possible all: 62.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TGT Resolution: 2.5→28.511 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 35.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.511 Å
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Refine LS restraints |
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LS refinement shell |
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