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- PDB-4k82: Crystal structure of lv-ranaspumin (Lv-RSN-1) from the foam nest ... -

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Basic information

Entry
Database: PDB / ID: 4k82
TitleCrystal structure of lv-ranaspumin (Lv-RSN-1) from the foam nest of Leptodactylus vastus, monoclinic crystal form
ComponentsLv-ranaspumin (Lv-RSN-1)
KeywordsSTRUCTURAL PROTEIN / alpha-helical / surfactant protein / foam nest / frog / amphibian
Function / homologyextracellular region / Ranaspumin
Function and homology information
Biological speciesLeptodactylus vastus (frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.6 Å
AuthorsHissa, D.C. / Bezerra, G.A. / Melo, V.M.M. / Gruber, K.
CitationJournal: 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
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lv-ranaspumin (Lv-RSN-1)


Theoretical massNumber of molelcules
Total (without water)23,4931
Polymers23,4931
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.874, 25.848, 66.076
Angle α, β, γ (deg.)90.000, 103.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lv-ranaspumin (Lv-RSN-1)


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.695.50.78111830733110.781100
1.69-1.795.50.491.51748031570.49100
1.79-1.915.60.2932.61641229530.293100
1.91-2.075.60.1684.31533527600.168100
2.07-2.265.50.11461399525380.114100
2.26-2.535.50.0946.91283423350.094100
2.53-2.925.40.0817.81108420420.081100
2.92-3.585.40.0767.9935717480.07699.9
3.58-5.065.30.0659728913740.06599.9
5.06-45.2594.90.069.137217670.0696.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
Arcimboldophasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1178 5.13 %random
Rwork0.1869 ---
obs0.1896 22971 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.7 Å2 / Biso mean: 31.7044 Å2 / Biso min: 14.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 0 215 1778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061630
X-RAY DIFFRACTIONf_angle_d1.0332199
X-RAY DIFFRACTIONf_chiral_restr0.067270
X-RAY DIFFRACTIONf_plane_restr0.004280
X-RAY DIFFRACTIONf_dihedral_angle_d12.344632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.67280.33591350.26727002835100
1.6728-1.7610.27281290.236827232852100
1.761-1.87130.30641530.218526972850100
1.8713-2.01570.2771530.195126902843100
2.0157-2.21850.26051470.172827172864100
2.2185-2.53920.22091390.181227332872100
2.5392-3.19820.24611480.192927442892100
3.1982-25.6320.21021740.17252789296399

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