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- PDB-2m0h: SP-B C-terminal (residues 59-80) peptide in methanol -

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Basic information

Entry
Database: PDB / ID: 2m0h
TitleSP-B C-terminal (residues 59-80) peptide in methanol
ComponentsPulmonary surfactant-associated protein B
KeywordsUNKNOWN FUNCTION / Pulmonary Surfactant-Associated Protein B / Peptide Fragments / Micelles / Dodecylphosphocholine
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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKuznetsova, A. / Long, J.R.
CitationJournal: To be Published
Title: Solution NMR structures of the C-terminal segment of surfactant protein B (residues 59-80) in DPC detergent micelles and methanol.
Authors: Kuznetsova, A. / Vanni, J. / Long, J.R.
History
DepositionOct 25, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)2,5361
Polymers2,5361
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 / 3000structures with favorable non-bond energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Pulmonary surfactant-associated protein B / SP-B / 18 kDa pulmonary-surfactant protein / 6 kDa protein / Pulmonary surfactant-associated ...SP-B / 18 kDa pulmonary-surfactant protein / 6 kDa protein / Pulmonary surfactant-associated proteolipid SPL(Phe)


Mass: 2536.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07988

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.2 mM protein, 20 mM TCEP, methanol / Solvent system: methanol
Sample
Conc. (mg/ml)ComponentSolution-ID
1.2 mMentity-11
20 mMTCEP-21
Sample conditionsIonic strength: 20 / pH: 4 / Pressure: ambient / Temperature units: 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
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
ProcheckNMRLaskowski and MacArthurgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
Details: INITIAL STRUCTURE CALCULATION WAS CARRIED OUT USING DEFAULT SCRIPT ANNEAL_NORDC.PY AND TEMPERATURE SCHEDULE 3500-TO-25 IN STEPS OF 12.5. REFINEMENT WAS PERFORMED FOR 3000 STRUCTURES USING ...Details: INITIAL STRUCTURE CALCULATION WAS CARRIED OUT USING DEFAULT SCRIPT ANNEAL_NORDC.PY AND TEMPERATURE SCHEDULE 3500-TO-25 IN STEPS OF 12.5. REFINEMENT WAS PERFORMED FOR 3000 STRUCTURES USING DEFAULT SCRIPT REFINE_NORDC.PY WITH TEMPERATURE SCHEDULES 1500-TO-25 IN STEPS OF 3.25 AND 500-TO-25 IN STEPS OF 2.25. FOR STRONGER J-COUPLING CONSTRAINTS ANNEALING DURING REFINEMENT ITS SCALING FACTOR IS RAMPED FROM 1 TO 3 DURING COOLING: JCOUP = CREATE_JCOUPPOT("JCOUP","JNA_COUP_SPBC_IN_METHANOL9.TBL", A=6.98,B=-1.38,C=1.72,PHASE=-60.0) RAMPEDPARAMS.APPEND( MULTRAMP(1,3, "JCOUP.SETSCALE( VALUE )") )
NMR constraintsNOE constraints total: 459 / NOE intraresidue total count: 217 / NOE long range total count: 4 / NOE medium range total count: 88 / NOE sequential total count: 96
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 3000 / Conformers submitted total number: 10

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