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- PDB-1dfw: CONFORMATIONAL MAPPING OF THE N-TERMINAL SEGMENT OF SURFACTANT PR... -

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Basic information

Entry
Database: PDB / ID: 1dfw
TitleCONFORMATIONAL MAPPING OF THE N-TERMINAL SEGMENT OF SURFACTANT PROTEIN B IN LIPID USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR)
ComponentsLUNG SURFACTANT PROTEIN B
KeywordsIMMUNE SYSTEM / LUNG SURFACTANT PROTEIN / SAPOSIN
Function / homology
Function and homology information


Defective pro-SFTPB causes SMDP1 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / sphingolipid metabolic process / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism ...Defective pro-SFTPB causes SMDP1 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / sphingolipid metabolic process / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism / multivesicular body / animal organ morphogenesis / lysosome / endoplasmic reticulum membrane / extracellular space / extracellular region
Similarity search - Function
Saposin A-type domain / Saposin / : / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 ...Saposin A-type domain / Saposin / : / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile.
Similarity search - Domain/homology
Pulmonary surfactant-associated protein B
Similarity search - Component
MethodINFRARED SPECTROSCOPY / molecular dynamics, simulated annealing
AuthorsGordon, L.M. / Lee, K.Y.C. / Lipp, M.M. / Zasadzinski, J.A. / Walther, F.J. / Sherman, M.A. / Waring, A.J.
CitationJournal: J.Pept.Res. / Year: 2000
Title: Conformational mapping of the N-terminal segment of surfactant protein B in lipid using 13C-enhanced Fourier transform infrared spectroscopy.
Authors: Gordon, L.M. / Lee, K.Y. / Lipp, M.M. / Zasadzinski, J.A. / Walther, F.J. / Sherman, M.A. / Waring, A.J.
History
DepositionNov 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LUNG SURFACTANT PROTEIN B


Theoretical massNumber of molelcules
Total (without water)2,9331
Polymers2,9331
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)10 / 15structures with acceptable covalent geometry
RepresentativeModel #8closest to the average

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Components

#1: Protein/peptide LUNG SURFACTANT PROTEIN B


Mass: 2932.701 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-25 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS)
References: UniProt: P07988

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Experimental details

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Experiment

ExperimentMethod: INFRARED SPECTROSCOPY
NMR experimentType: 13-C isotope enhanced FTIR
NMR detailsText: 13-C isotope enhanced FTIR study. The coordinates in this entry were generated from 13-C induced spectral shifts which give residue-specific secondary structure information.

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Sample preparation

CrystalDescription: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES ...Description: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 1,3,5,8,10,11,13,14,15,16,18,25. SOLVENT SYSTEM: LIPOSOMES OF 1-PALMITOYL-2-OLEOYL PHOSPHATIDYLGLYCEROL (POPG). SAMPLE CONDITIONS: 298 K, 1 ATM, PH 7.4, IONIC STRENGTH 10 MM PHOSPHATE. TOTAL NUMBER OF CONFORMERS CALCULATED: 15; TOTAL NUMBER OF CONFORMERS SUBMITTED: 10; REPRESENTATIVE CONFORMER 8 (CLOSEST TO THE AVERAGE). SPECTROMETER: MATTSON FTIR RESEARCH SERIES. REFINEMENT METHOD: MOLECULAR DYNAMICS, SIMULATED ANNEALING. SOFTWARE: WINFIRST (FTIR CURVE FITTING SOFTWARE), DISCOVER 2.9.7, MOLECULAR SIMULATIONS, INC. (SAN DIEGO, CA).
DetailsContents: This structure was determined using 13-C isotope enhanced FTIR spectroscopy on a family of selectively labeled chemically synthesized peptides. 13-C carbonyl labels included residues ...Contents: This structure was determined using 13-C isotope enhanced FTIR spectroscopy on a family of selectively labeled chemically synthesized peptides. 13-C carbonyl labels included residues 1,3,5,8,10,11,13,14,15,16,18,25.
Solvent system: Liposomes of 1-palmitoyl-2-oleoyl phosphatidylglycerol (POPG)
Sample conditionsIonic strength: 10 mM phosphate / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: FTIR

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Data collection

NMR spectrometerType: Mattson FTIR Research Series / Manufacturer: Mattson FTIR / Model: Research Series

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Processing

NMR software
NameVersionDeveloperClassification
Winfirst(FTIR curve fitting software)Kauppine et al.data analysis
Discover2.9.7Molecular Simulations, Inc. (San Diego, CA)refinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: Molecular dynamics (simulated annealing) was used to generate an ensemble of conformers consistent with the FTIR data.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 15 / Conformers submitted total number: 10

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