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Yorodumi- PDB-4dvt: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dvt | ||||||
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Title | Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AS-II-37 | ||||||
Components | clade A/E 93TH057 HIV-1 gp120 core | ||||||
Keywords | viral protein/transcription inhibitor / HIV-1 gp120 / small molecule inhibitor / CD4 binding site / AS-II-37 / viral protein-transcription inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kwon, Y.D. / Kwong, P.D. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site. Authors: Kwon, Y.D. / Lalonde, J.M. / Yang, Y. / Elban, M.A. / Sugawara, A. / Courter, J.R. / Jones, D.M. / Smith, A.B. / Debnath, A.K. / Kwong, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dvt.cif.gz | 297.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dvt.ent.gz | 244 KB | Display | PDB format |
PDBx/mmJSON format | 4dvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dvt_validation.pdf.gz | 892.1 KB | Display | wwPDB validaton report |
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Full document | 4dvt_full_validation.pdf.gz | 916.4 KB | Display | |
Data in XML | 4dvt_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 4dvt_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/4dvt ftp://data.pdbj.org/pub/pdb/validation_reports/dv/4dvt | HTTPS FTP |
-Related structure data
Related structure data | 4dvrC 4dvsC 4dvvC 4dvwC 4dvxC 3tgtS 4dvu 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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1 |
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2 |
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Unit cell |
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Details | monomer |
-Components
#1: Protein | Mass: 39160.367 Da / Num. of mol.: 2 / Mutation: S375H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9 #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CRYSTALLIZED SEQUENCE WAS CONSTRUCTED BY DELETION OF N-TERMINAL 1-43, BY REPLACING THE V1/V2 ...THE CRYSTALLIZ | |
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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: 2.66 Å3/Da / Density % sol: 53.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 8000, 5% iso-propanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 29562 / Num. obs: 27759 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 45.16 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.085 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.46 / Rsym value: 0.485 / % possible all: 60 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TGT Resolution: 2.4→28.192 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.42 / Phase error: 30.27 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.4336 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→28.192 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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