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- PDB-1kmr: Solution NMR Structure of Surfactant Protein B (11-25) (SP-B11-25) -

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Basic information

Entry
Database: PDB / ID: 1kmr
TitleSolution NMR Structure of Surfactant Protein B (11-25) (SP-B11-25)
ComponentsPULMONARY SURFACTANT-ASSOCIATED PROTEIN B
KeywordsLIPID BINDING PROTEIN / HELIX
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
MethodSOLUTION NMR / simulated annealing
AuthorsKurutz, J.W. / Lee, K.Y.C.
CitationJournal: Biochemistry / Year: 2002
Title: NMR structure of lung surfactant peptide SP-B(11-25).
Authors: Kurutz, J.W. / Lee, K.Y.
History
DepositionDec 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)1,7021
Polymers1,7021
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)17 / 78structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PULMONARY SURFACTANT-ASSOCIATED PROTEIN B / SP-B / Pulmonary surfactant-associated proteolipid SPL(Phe) / 18 kDa pulmonary-surfactant protein


Mass: 1702.183 Da / Num. of mol.: 1
Fragment: SEQUENCE DATABASE RESIDUES 211-225, NUMBERED 11-25
Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS (HUMANS).
References: UniProt: P07988

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: WET water suppression

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Sample preparation

DetailsContents: 1.25 mM peptide, 0.1 mM DSS-d6
Solvent system: Partially deuterated methanol (CD3OH), 98% D
Sample conditionsIonic strength: no additional salt or buffer / pH: 5.5 / Pressure: ambient / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian Associates, Inc.collection
VNMR6.1BVarian Associates, Inc.processing
VNMR6.1BVarian Associates, Inc.data analysis
Discover2.98MSI/BIOSYM/Accelrysstructure solution
Insight II98MSI/BIOSYM/Accelrysstructure solution
Insight II98MSI/BIOSYM/Accelrysrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 78 / Conformers submitted total number: 17

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