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- PDB-4k83: Crystal structure of lv-ranaspumin (Lv-RSN-1) from the foam nest ... -

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Basic information

Entry
Database: PDB / ID: 4k83
TitleCrystal structure of lv-ranaspumin (Lv-RSN-1) from the foam nest of Leptodactylus vastus, orthorhombic 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.662, 52.900, 102.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 204 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9497 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2012 / Details: mirrors
RadiationMonochromator: Bartels / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9497 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.75-1.8426.20.51.60.5198.7
1.84-1.9626.50.2782.80.278198.9
1.96-2.0925.20.1445.40.144199.6
2.09-2.2626.90.0918.40.091199.4
2.26-2.4726.80.068110.068199.7
2.47-2.7725.60.05213.80.052199.8
2.77-3.223.10.04115.90.041199.8
3.2-3.9124.80.03418.40.0341100
3.91-5.5322.30.03200.031100
5.53-47.0321.20.027140.027199.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K82

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
RfactorNum. reflection% reflection
Rfree0.2492 1065 5.15 %
Rwork0.2003 --
obs0.2026 20684 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.2769 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 0 204 1754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071596
X-RAY DIFFRACTIONf_angle_d1.1092149
X-RAY DIFFRACTIONf_dihedral_angle_d12.593619
X-RAY DIFFRACTIONf_chiral_restr0.073265
X-RAY DIFFRACTIONf_plane_restr0.004271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.82970.32031270.25362380X-RAY DIFFRACTION98
1.8297-1.92610.29511370.24792396X-RAY DIFFRACTION99
1.9261-2.04680.31491250.23232393X-RAY DIFFRACTION99
2.0468-2.20480.27441560.21982396X-RAY DIFFRACTION99
2.2048-2.42670.24871500.2012431X-RAY DIFFRACTION99
2.4267-2.77780.23891270.20662460X-RAY DIFFRACTION100
2.7778-3.49960.26431240.20282509X-RAY DIFFRACTION100
3.4996-47.04650.21321190.17842654X-RAY DIFFRACTION100

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