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Yorodumi- PDB-4hlr: Structural Determinants of Trimerization Specificity in HIV-1 gp4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hlr | ||||||
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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 | Retroviral envelope protein / Retroviral envelope protein GP41-like / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane / HEXANE-1,6-DIOL / Env polyprotein Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 | 4hlr.cif.gz | 25.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hlr.ent.gz | 16.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hlr_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
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Full document | 4hlr_full_validation.pdf.gz | 424 KB | Display | |
Data in XML | 4hlr_validation.xml.gz | 4 KB | Display | |
Data in CIF | 4hlr_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/4hlr ftp://data.pdbj.org/pub/pdb/validation_reports/hl/4hlr | HTTPS FTP |
-Related structure data
Related structure data | 3u91SC 3uiaC 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/peptide | Mass: 3936.581 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN / Mutation: I14L, L17I 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 |
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#2: Chemical | ChemComp-HEZ / |
#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: 5.6 Details: 2.5M 1,6-Hexanediol, 0.1M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→42.1 Å / Num. all: 6325 / Num. obs: 6325 / % possible obs: 87.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 5.6 / Num. unique all: 692 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U91 Resolution: 1.57→42.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.149 / SU ML: 0.057 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 28.957 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→42.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.612 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -21.247 Å / Origin y: 7.011 Å / Origin z: 11.626 Å
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