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- PDB-1byv: GLYCOSYLATED EEL CALCITONIN -

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Basic information

Entry
Database: PDB / ID: 1byv
TitleGLYCOSYLATED EEL CALCITONIN
ComponentsPROTEIN (CALCITONIN)
KeywordsHORMONE/GROWTH FACTOR / HOROMONE / CALCIUM-REGULATOR / OSTEOPOROSIS / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


hormone activity / extracellular region
Similarity search - Function
Calcitonin / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family
Similarity search - Domain/homology
Biological speciesAnguilla japonica (Japanese eel)
MethodSOLUTION NMR / distance geometry
AuthorsHashimoto, Y. / Toma, K. / Nishikido, J. / Yamamoto, K. / Haneda, K. / Inazu, T. / Valentine, K.G. / Opella, S.J.
CitationJournal: Biochemistry / Year: 1999
Title: Effects of glycosylation on the structure and dynamics of eel calcitonin in micelles and lipid bilayers determined by nuclear magnetic resonance spectroscopy.
Authors: Hashimoto, Y. / Toma, K. / Nishikido, J. / Yamamoto, K. / Haneda, K. / Inazu, T. / Valentine, K.G. / Opella, S.J.
History
DepositionOct 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_software / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CALCITONIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6412
Polymers3,4201
Non-polymers2211
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 / 20VIOLATION
Representative

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Components

#1: Protein/peptide PROTEIN (CALCITONIN)


Mass: 3419.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SYNTHETICALLY GLYCOLYLATED AT ASN3 / Source: (natural) Anguilla japonica (Japanese eel) / References: UniProt: P01262
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING A SERIES OF 2D NRM SPECTROSCOPY ON UNLABLED SAMPLE. SODIUM DODECYL SULFATE (SDS) WAS ADDED TO THE NMR SAMPLE AT A SDS/ PEPTIDE MOLAR RATIO OF 100/1.

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Sample preparation

Sample conditionspH: 4.5 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX750 / Manufacturer: Bruker / Model: DMX750 / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
DGIIHAVELrefinement
Felixstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: VIOLATION / Conformers calculated total number: 20 / Conformers submitted total number: 10

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