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Yorodumi- PDB-4dvx: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dvx | ||||||
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Title | Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with MAE-II-188 | ||||||
Components | clade A/E 93TH057 HIV-1 gp120 core | ||||||
Keywords | viral protein/transcription inhibitor / HIV-1 gp120 / small molecule inhibitor / CD4 binding site / MAE-II-188 / 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 | 4dvx.cif.gz | 295.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dvx.ent.gz | 243.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dvx_validation.pdf.gz | 849.4 KB | Display | wwPDB validaton report |
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Full document | 4dvx_full_validation.pdf.gz | 873.5 KB | Display | |
Data in XML | 4dvx_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 4dvx_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/4dvx ftp://data.pdbj.org/pub/pdb/validation_reports/dv/4dvx | HTTPS FTP |
-Related structure data
Related structure data | 4dvrC 4dvsC 4dvtC 4dvvC 4dvwC 4dvu 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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2 |
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Unit cell |
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-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 / | Has protein modification | Y | |
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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: 2.65 Å3/Da / Density % sol: 53.51 % |
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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 source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
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Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 23, 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: 32234 / Num. obs: 26948 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 41.97 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.076 / Net I/σ(I): 16.34 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.48 / % possible all: 27.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→28.461 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.37 / Phase error: 33.43 / 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: 64.1823 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→28.461 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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