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- PDB-2dwf: NMR structure of Mini-B, an N-terminal- C-terminal construct from... -

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Basic information

Entry
Database: PDB / ID: 2dwf
TitleNMR structure of Mini-B, an N-terminal- C-terminal construct from human Surfactant Protein B (SP-B), in Sodium dodecyl sulfate (SDS) micelles
ComponentsPulmonary surfactant-associated protein B
KeywordsSURFACE ACTIVE PROTEIN / Mini-B / SP-B / Surfactant Protein B / Lipid associated protein
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 / sphingolipid metabolic process / 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 / clathrin-coated endocytic vesicle / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / 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 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, Molecular dynamics
AuthorsBooth, V. / Sarker, M. / Waring, A.J. / Keough, K.M.W.
CitationJournal: To be Published
Title: NMR structure of Mini-B, an N-terminal - C-terminal construct from human Surfactant Protein B (SP-B), in Sodium dodecyl sulfate (SDS) micelles
Authors: Booth, V. / Sarker, M. / Waring, A.J. / Keough, K.M.W.
History
DepositionAug 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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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: Mini-B / Source method: obtained synthetically
Details: This sequence is a biologically active fragment of the protein SP-B which occurs naturally in humans.
References: UniProt: P07988
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
1413D 15N-separated TOCSY

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Sample preparation

DetailsContents: Partially 15N-labelled peptide with 15N labels on Leucine (3, 7, 22, 25, 29, 31), Alanine (6, 13) and Glycine (18); 1.5mM peptide, 150mM SDS, 0.4mM DSS, 90% H2O, 10% D2O
Solvent system: 150mM SDS, 0.4mM DSS, 90% H2O, 10% D2O
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglioprocessing
Sparky3.11Goddard and Knellerdata analysis
CNS1.1Brungerrefinement
MOLMOL2K.2Koradidata analysis
RefinementMethod: Simulated annealing, Molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 15

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