+Open data
-Basic information
Entry | Database: PDB / ID: 1lcs | |||||||||
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Title | RECEPTOR-BINDING DOMAIN FROM SUBGROUP B FELINE LEUKEMIA VIRUS | |||||||||
Components | FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN | |||||||||
Keywords | VIRAL PROTEIN / antiparallel beta-sandwich glycoprotein | |||||||||
Function / homology | Function and homology information membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||
Biological species | Feline leukemia virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Barnett, A.L. / Wensel, D.L. / Li, W. / Fass, D. / Cunningham, J.M. | |||||||||
Citation | Journal: J.Virol. / Year: 2003 Title: Structure and Mechanism of a Coreceptor for Infection by a pathogenic feline retrovirus Authors: Barnett, A.L. / Wensel, D.L. / Li, W. / Fass, D. / Cunningham, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lcs.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lcs.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lcs ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lcs | HTTPS FTP |
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-Related structure data
Related structure data | 1aolS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23410.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Feline leukemia virus / Genus: Gammaretrovirus / Strain: strain B/lambda-B1 / Gene: ENV / Plasmid: PVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 AND HI5 / References: GenBank: 323911, UniProt: P11261*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1- ...2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-TOE / | #5: Water | ChemComp-HOH / | |
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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: 3.11 Å3/Da / Density % sol: 60.46 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 21072 / Num. obs: 21010 / % possible obs: 99.7 % / Redundancy: 9 % / Rsym value: 0.061 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 9.4 / Rsym value: 0.192 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 21072 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 100 % / Rmerge(I) obs: 0.192 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AOL Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 7 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |