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Yorodumi- PDB-4k83: Crystal structure of lv-ranaspumin (Lv-RSN-1) from the foam nest ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k83 | ||||||
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Title | Crystal structure of lv-ranaspumin (Lv-RSN-1) from the foam nest of Leptodactylus vastus, orthorhombic crystal form | ||||||
Components | Lv-ranaspumin (Lv-RSN-1) | ||||||
Keywords | STRUCTURAL PROTEIN / alpha-helical / surfactant protein / foam nest / frog / amphibian | ||||||
Function / homology | extracellular region / Ranaspumin Function and homology information | ||||||
Biological species | Leptodactylus vastus (frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Hissa, D.C. / Bezerra, G.A. / Melo, V.M.M. / Gruber, K. | ||||||
Citation | Journal: Chembiochem / Year: 2014 Title: Unique Crystal Structure of a Novel Surfactant Protein from the Foam Nest of the Frog Leptodactylus vastus. Authors: Cavalcante Hissa, D. / Arruda Bezerra, G. / Birner-Gruenberger, R. / Paulino Silva, L. / Uson, I. / Gruber, K. / Maciel Melo, V.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k83.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k83.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 4k83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k83_validation.pdf.gz | 422.6 KB | Display | wwPDB validaton report |
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Full document | 4k83_full_validation.pdf.gz | 424.6 KB | Display | |
Data in XML | 4k83_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4k83_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/4k83 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/4k83 | HTTPS FTP |
-Related structure data
Related structure data | 4k82SC 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 | Mass: 23492.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: foam nest / Source: (natural) Leptodactylus vastus (frog) / References: UniProt: P85507*PLUS |
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#2: 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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.25 M sodium acetate, 28% PEG 3350, pH 8.0, vapour diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9497 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Bartels / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9497 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→51.359 Å / Num. all: 20733 / Num. obs: 20733 / % possible obs: 99.5 % / Redundancy: 25.4 % / Rsym value: 0.044 / Net I/σ(I): 43.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4K82 Resolution: 1.75→47.03 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.24 / σ(F): 1.36 / Phase error: 24.92 / 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: 16.2769 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→47.03 Å
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Refine LS restraints |
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LS refinement shell |
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