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- PDB-1ssz: Conformational Mapping of Mini-B: An N-terminal/C-terminal Constr... -

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Entry
Database: PDB / ID: 1ssz
TitleConformational Mapping of Mini-B: An N-terminal/C-terminal Construct of Surfactant Protein B Using 13C-Enhanced Fourier Transform Infrared (FTIR) Spectroscopy
ComponentsPulmonary surfactant-associated protein B
KeywordsSURFACE ACTIVE PROTEIN / 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 / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / sphingolipid metabolic process / 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 / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / sphingolipid metabolic process / Surfactant metabolism / multivesicular body / animal organ morphogenesis / lysosome / endoplasmic reticulum membrane / 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 (B) Domains ...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
Biological speciesHomo sapiens (human)
MethodINFRARED SPECTROSCOPY / distance geometry, simulated annealing
AuthorsWaring, A.J. / Walther, F.J. / Gordon, L.M. / Hernandez-Juviel, J.M. / Hong, T. / Sherman, M.A. / Alonso, C. / Alig, T. / Braun, A. / Bacon, D. / Zasadzinski, J.A.
CitationJournal: J.Pept.Res. / Year: 2005
Title: The role of charged amphipathic helices in the structure and function of surfactant protein B.
Authors: Waring, A.J. / Walther, F.J. / Gordon, L.M. / Hernandez-Juviel, J.M. / Hong, T. / Sherman, M.A. / Alonso, C. / Alig, T. / Braun, A. / Bacon, D. / Zasadzinski, J.A.
History
DepositionMar 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_entity_src_syn / pdbx_nmr_details / pdbx_nmr_exptl / pdbx_nmr_refine / struct
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_exptl.conditions_id / _pdbx_nmr_refine.method / _pdbx_nmr_refine.software_ordinal / _struct.title
Remark 250EXPERIMENTAL DETAILS. EXPERIMENT TYPE : INFRARED SPECTROSCOPY. TEMPERATURE : 298 PRESSURE : ambient ...EXPERIMENTAL DETAILS. EXPERIMENT TYPE : INFRARED SPECTROSCOPY. TEMPERATURE : 298 PRESSURE : ambient SAMPLE 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 3,6,7,8,11,13,15,16,18,19,22,25,26,29,30. peptide self-film solvated with hexafluoroispropanol:D20, 9:1 FTIR EXPERIMENTS CONDUCTED : distance geometry; simulated annealing SPECTROMETER MODEL : vector 22 FTIR SPECTROMETER MANUFACTURER : BRUKER STRUCTURE DETERMINATION. SOFTWARE USED : Winfirst, MODELLER 6.3, CHARMM 22 METHOD USED : distance geometry; simulated annealing CONFORMERS, NUMBER CALCULATED : 75 CONFORMERS, NUMBER SUBMITTED : 10 CONFORMERS, SELECTION CRITERIA : structures with acceptable covalent geometry BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM 13-C INDUCED SPECTRAL SHIFTS WHICH GIVE RESIDUE-SPECIFIC SECONDARY STRUCTURE INFORMATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pulmonary surfactant-associated protein B


Theoretical massNumber of molelcules
Total (without water)3,9341
Polymers3,9341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 75structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Pulmonary surfactant-associated protein B / SP-B / 6 kDa protein / Pulmonary surfactant-associated proteolipid SPLPhe / 18 kDa pulmonary- ...SP-B / 6 kDa protein / Pulmonary surfactant-associated proteolipid SPLPhe / 18 kDa pulmonary-surfactant protein


Mass: 3934.022 Da / Num. of mol.: 1 / Fragment: residues 208-218, 263-278 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07988

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Experimental details

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Experiment

ExperimentMethod: INFRARED SPECTROSCOPY
NMR experimentType: FTIR

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Sample preparation

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 3,6,7,8,11,13,15,16,18,19,22,25,26,29,30.
Solvent system: peptide self-film solvated with hexafluoroispropanol:D20, 9:1
Sample conditionsPressure: ambient / Temperature: 298

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Data collection

NMR spectrometerType: Bruker vector 22 FTIR / Manufacturer: Bruker / Model: vector 22 FTIR

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Processing

NMR software
NameVersionDeveloperClassification
WinfirstFTIR curve fitting softwareKauppine et al.data analysis
MODELLER6.2Sali et al.structure solution
CHARMM22Brooks et al.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 3
Details: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM 13-C INDUCED SPECTRAL SHIFTS WHICH GIVE RESIDUE-SPECIFIC SECONDARY STRUCTURE INFORMATION.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 75 / Conformers submitted total number: 10

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