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- PDB-1q3m: 1H NMR structure bundle of bovine Ca2+-osteocalcin -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1q3m
Title1H NMR structure bundle of bovine Ca2+-osteocalcin
ComponentsOsteocalcin
KeywordsCalcium-binding protein / Bone Protein / calcium binding protein
Function / homology
Function and homology information


structural constituent of bone / hydroxyapatite binding / negative regulation of bone development / biomineral tissue development / regulation of testosterone biosynthetic process / response to vitamin K / type B pancreatic cell proliferation / regulation of bone mineralization / positive regulation of neurotransmitter secretion / regulation of cellular response to insulin stimulus ...structural constituent of bone / hydroxyapatite binding / negative regulation of bone development / biomineral tissue development / regulation of testosterone biosynthetic process / response to vitamin K / type B pancreatic cell proliferation / regulation of bone mineralization / positive regulation of neurotransmitter secretion / regulation of cellular response to insulin stimulus / bone development / hormone activity / brain development / cognition / osteoblast differentiation / cellular response to insulin stimulus / glucose homeostasis / learning or memory / calcium ion binding / extracellular region / cytoplasm
Similarity search - Function
Osteocalcin/matrix Gla protein / Osteocalcin / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues.
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, energy minimization
AuthorsDowd, T.L. / Rosen, J.F. / Li, L. / Gundberg, C.M.
CitationJournal: Biochemistry / Year: 2003
Title: The Three-Dimensional Structure of Bovine Calcium Ion-Bound Osteocalcin Using 1H NMR Spectroscopy
Authors: Dowd, T.L. / Rosen, J.F. / Li, L. / Gundberg, C.M.
History
DepositionJul 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)5,8421
Polymers5,8421
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)13 / -structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: Protein/peptide Osteocalcin / Gamma-carboxyglutamic acid-containing protein / Bone Gla-protein / BGP


Mass: 5842.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bone powder / Source: (natural) Bos taurus (cattle) / References: UniProt: P02820

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
12117 and 60 ms mixing time TOCSYs
131NOESY (150 ms)
NMR detailsText: Since the 15 N-terminal residues are unstructured and not constrained, only the structured region of the molecule (residues 16-49) is included in the structure bundle. All of the structures ...Text: Since the 15 N-terminal residues are unstructured and not constrained, only the structured region of the molecule (residues 16-49) is included in the structure bundle. All of the structures were solved in the presence of 6 mM CaCl2.

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Sample preparation

DetailsContents: 20mM NaCl, 6mM Ca(Cl)2, 0.25mM DSS / Solvent system: 10% 2H2O
Sample conditionsIonic strength: 38 / pH: 6.9 / Pressure: 1 atm / Temperature: 310 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: Bruker drx600 / Manufacturer: Bruker / Model: drx600 / Field strength: 600 MHz

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Processing

SoftwareName: CNS / Classification: refinement
NMR software
NameDeveloperClassification
CNSBrunger, A.T.refinement
DYANAstructure solution
TALOSdata analysis
AQUAdata analysis
PROCHECKdata analysis
RefinementMethod: torsion angle dynamics, simulated annealing, energy minimization
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers submitted total number: 13

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