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- PDB-4k82: Crystal structure of lv-ranaspumin (Lv-RSN-1) from the foam nest ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4k82 | ||||||
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Title | Crystal structure of lv-ranaspumin (Lv-RSN-1) from the foam nest of Leptodactylus vastus, monoclinic crystal form | ||||||
![]() | Lv-ranaspumin (Lv-RSN-1) | ||||||
![]() | STRUCTURAL PROTEIN / alpha-helical / surfactant protein / foam nest / frog / amphibian | ||||||
Function / homology | extracellular region / Ranaspumin![]() | ||||||
Biological species | Leptodactylus vastus (frog) | ||||||
Method | ![]() ![]() | ||||||
![]() | Hissa, D.C. / Bezerra, G.A. / Melo, V.M.M. / Gruber, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.8 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.2 KB | Display | ![]() |
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Full document | ![]() | 424.2 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.2 M Potassium formate, 20% (w/v) PEG 3350, pH 7.3, vapour diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2012 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→64.119 Å / Num. all: 22985 / Num. obs: 22985 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rsym value: 0.086 / Net I/σ(I): 9.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.6→25.629 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.7837 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 27.98 / 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 max: 79.7 Å2 / Biso mean: 31.7044 Å2 / Biso min: 14.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→25.629 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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