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- PDB-2wgo: Structure of ranaspumin-2, a surfactant protein from the foam nes... -

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Basic information

Entry
Database: PDB / ID: 2wgo
TitleStructure of ranaspumin-2, a surfactant protein from the foam nests of a tropical frog
ComponentsRANASPUMIN-2
KeywordsSURFACTANT PROTEIN / CYSTATIN FOLD
Function / homologyNuclear Transport Factor 2; Chain: A, - #260 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Ranaspumin-2
Function and homology information
Biological speciesENGYSTOMOPS PUSTULOSUS (Tungara frog)
MethodSOLUTION NMR / ARIA-ALIKE
AuthorsMackenzie, C.D. / Smith, B.O. / Kennedy, M.W. / Cooper, A.
Citation
Journal: Biophys.J. / Year: 2009
Title: Ranaspumin-2: Structure and Function of a Surfactant Protein from the Foam Nests of a Tropical Frog.
Authors: Mackenzie, C.D. / Smith, B.O. / Meister, A. / Blume, A. / Zhao, X. / Lu, J.R. / Kennedy, M.W. / Cooper, A.
#1: Journal: Ph D Thesis / Year: 2007
Title: The Biophysical Chemistry of Frog Foam Nest Proteins
Authors: Mackenzie, C.D.
History
DepositionApr 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RANASPUMIN-2


Theoretical massNumber of molelcules
Total (without water)11,2871
Polymers11,2871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #17

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Components

#1: Protein RANASPUMIN-2 / RSN-2


Mass: 11286.918 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-97
Source method: isolated from a genetically manipulated source
Details: RANASPUMIN-2 WITH AN AMPHIPHILIC AMINO ACID SEQUENCE, EXHIBITS SUBSTANTIAL DETERGENT-LIKE SURFACTANT ACTIVITY NECESSARY FOR PRODUCTION OF FOAM, YET IS HARMLESS TO THE MEMBRANES OF EGGS AND SPERMATOZOA
Source: (gene. exp.) ENGYSTOMOPS PUSTULOSUS (Tungara frog) / Organ: OVIDUCT / Plasmid: PCRT7/NT-TOPO BASED HIS6-THROMBIN-RSN-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5DCK2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCA(CO)NH
121CC(CO)NH
131(HB)CB(CGCDCE)HE
141(HB)CB(CGCD)HD
151HN(CA)CB
161HN(CA)CO
171HNCO
181HSQC 308K
191HBHA(CO)NH
1101HNHAHB
1111HSQC 303K
112113C HSQC
113113C NOESY
114115N-NOESY(2)
1151(H)CCH- TOCSY
1161HSQC PRE D2O
1171HSQC CN2
1181HSQC T=0 D2O
1191HSQC T=15 D2O
1201HSQC T=30 D2O
1211HSQC T=45 D2O
1221HSQC T=60 D2O
1231HSQC T=75 D2O
1241HSQC T=90 D2O
1251HSQC T=105 D2O
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED RSN-2.

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Sample preparation

DetailsContents: RSN-2 0.001000 M, NACL 0.050000 M, NAPI 0.020000 M, D2O 0.050000 M3/M3CN1
Sample conditionsIonic strength: 70 mM / pH: 7 / Pressure: 1.0 atm / Temperature: 308.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, READ,RICE,SIMONSON,WARRENrefinement
CcpNmr AnalysisANALYSISstructure solution
TopSpinstructure solution
CNSstructure solution
CcpNmr AnalysisANALYSISstructure solution
Azarastructure solution
RefinementMethod: ARIA-ALIKE / Software ordinal: 1
Details: ARIA-ALIKE ITERATIVE ASSIGNMENT INCLUDING PROCHIRAL SWAPPING WITH A METROPOLIS ACCEPTANCE CRITERION. PARALLHDG 5.3 FORCEFIELD.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 25

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