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- PDB-2glh: Solution Conformation of Salmon Calcitonin in Sodium Dodecyl Sulf... -

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Basic information

Entry
Database: PDB / ID: 2glh
TitleSolution Conformation of Salmon Calcitonin in Sodium Dodecyl Sulfate Micelles
ComponentsCalcitonin-1
KeywordsHORMONE/GROWTH FACTOR / a-helix / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


calcitonin receptor binding / sperm capacitation / activation of adenylate cyclase activity / hormone activity / extracellular space
Similarity search - Function
Calcitonin / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family
Similarity search - Domain/homology
MethodSOLUTION NMR / restrained simulated annealing, energy minimization, unrestrained molecular dynamics
AuthorsAndreotti, G. / Lopez-Mendez, B. / Amodeo, P. / Morelli, M.A. / Nakamuta, H. / Motta, A.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Structural determinants of salmon calcitonin bioactivity: the role of the Leu-based amphipathic alpha-helix.
Authors: Andreotti, G. / Mendez, B.L. / Amodeo, P. / Morelli, M.A. / Nakamuta, H. / Motta, A.
#1: Journal: J.Biomol.NMR / Year: 1999
Title: Conformational flexibility in calcitonin: The dynamic properties of human and salmon calcitonin in solution
Authors: Amodeo, P. / Motta, A. / Strazzullo, G. / Castiglione-Morelli, M.A.
#2: Journal: Biochemistry / Year: 1991
Title: Solution Conformation of Salmon Calcitonin in Sodium Dodecyl Sulfate Micelles As Determined by Two-Dimensional NMR and Distance Geometry Calculations
Authors: Motta, A. / Pastore, A. / Goud, N.A. / Castiglione-Morelli, M.A.
History
DepositionApr 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Calcitonin-1


Theoretical massNumber of molelcules
Total (without water)3,4371
Polymers3,4371
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)100 / 100periodically sampled unrestrained molecular dynamics structures
RepresentativeModel #1

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Components

#1: Protein/peptide Calcitonin-1


Mass: 3436.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide synthesis / References: UniProt: P01263
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
131DQF-COSY
2412D NOESY
2512D TOCSY
261DQF-COSY

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Sample preparation

DetailsContents: 5 mM sCT; 20 mM phosphate buffer; 600 mM SDS; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
14.1AMBIENT 310 K
27.2AMBIENT 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionClassification
XwinNMRprocessing
AURELIAdata analysis
Amber6structure solution
Amber6refinement
RefinementMethod: restrained simulated annealing, energy minimization, unrestrained molecular dynamics
Software ordinal: 1
NMR ensembleConformer selection criteria: periodically sampled unrestrained molecular dynamics structures
Conformers calculated total number: 100 / Conformers submitted total number: 100

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