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Yorodumi- PDB-3u91: Structural Determinants of Trimerization Specificity in HIV-1 gp4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u91 | ||||||
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Title | Structural Determinants of Trimerization Specificity in HIV-1 gp41 Protein | ||||||
Components | Gp41 | ||||||
Keywords | VIRAL PROTEIN / gp41 / HIV-1 / trimerization domain / oligomeric structure | ||||||
Function / homology | Function and homology information membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Liu, J. / Lu, M. | ||||||
Citation | Journal: To be Published Title: Structural Determinants of Trimerization Specificity in HIV-1 gp41 Protein Authors: Liu, J. / Li, Q. / Dey, A.K. / Moore, J.P. / Lu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u91.cif.gz | 26.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u91.ent.gz | 16.5 KB | Display | PDB format |
PDBx/mmJSON format | 3u91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u91_validation.pdf.gz | 741.3 KB | Display | wwPDB validaton report |
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Full document | 3u91_full_validation.pdf.gz | 741.8 KB | Display | |
Data in XML | 3u91_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 3u91_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/3u91 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/3u91 | HTTPS FTP |
-Related structure data
Related structure data | 3uiaC 4hlrC 1aikS 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 3936.581 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YYZ1, UniProt: Q7ZC55*PLUS |
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#2: Chemical | ChemComp-JEF / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% Jeffamine M600, 0.1M MES, 25mM Cesium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9676 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9676 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→42.14 Å / Num. obs: 9173 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 6.4 / Rsym value: 0.467 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AIK Resolution: 1.45→42.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.818 / SU ML: 0.037 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.142 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→42.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.489 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -21.502 Å / Origin y: 6.958 Å / Origin z: -8.623 Å
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