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- PDB-2nln: Solution Structure of Calcium-free Rat Beta-parvalbumin -

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Basic information

Entry
Database: PDB / ID: 2nln
TitleSolution Structure of Calcium-free Rat Beta-parvalbumin
ComponentsOncomodulin
KeywordsMETAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN / RAT BETA PARVALBUMIN / RAT ONCOMODULIN
Function / homology
Function and homology information


cuticular plate / stereocilium / ion binding / supramolecular fiber / cochlea development / response to wounding / vesicle / calcium ion binding / protein-containing complex binding / protein homodimerization activity ...cuticular plate / stereocilium / ion binding / supramolecular fiber / cochlea development / response to wounding / vesicle / calcium ion binding / protein-containing complex binding / protein homodimerization activity / protein-containing complex / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Parvalbumin / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...Parvalbumin / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing using torsion angle molecular dynamics
AuthorsHenzl, M.T.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure of Ca2+-free rat beta-parvalbumin (oncomodulin).
Authors: Henzl, M.T. / Tanner, J.J.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Oncomodulin


Theoretical massNumber of molelcules
Total (without water)12,0671
Polymers12,0671
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)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Oncomodulin / OM / Parvalbumin beta


Mass: 12067.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ocm / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P02631

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
13315N-IPAP-HSQC
14415N-HSQC
151HNHA
NMR detailsText: This structure was determined using: 1. distance restraints collected from 3D NOESY experiments, 2. dihedral angle restraints based on coupling constants (HNHA), and chemical shift data (CSI, ...Text: This structure was determined using: 1. distance restraints collected from 3D NOESY experiments, 2. dihedral angle restraints based on coupling constants (HNHA), and chemical shift data (CSI, TALOS), 3. hydrogen-bond restraints (collected from H-D exchange measurements), 4. 1H-15N residual dipolar couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
14 mM oncomodulin, U-15N, 0.15 M NaCl, 0.01 M Mes, pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
24 mM oncomodulin, U-15N, 13C, 0.15 M NaCl, 0.01 M Mes, pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
34 mM oncomodulin, U-15N, 0.15 M NaCl, 0.01 M Mes, pH 6.0, 13 mg/mL Pf1 bacteriophage, 90% H2O, 10% D2O90% H2O/10% D2O
44 mM oncomodulin, U-15N, 0.15 M NaCl, 0.01 M Mes, pD 6.2, 100% D2O100% D2O
Sample conditionsIonic strength: 0.15 M NaCl, 0.01 M Mes / pH: 6.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRvariancollection
NMRPipeDelaglio, F. et al.processing
SparkyGoddard T.D., Kneller, D.G.data analysis
ARIA2.0aNilges, M. et al.structure solution
CNS1.1Brunger, A.T. et al.structure solution
CNS1.1Brunger, A.T. et al.refinement
RefinementMethod: simulated annealing using torsion angle molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 2961 restraints: 2553 are NOE-derived distance constraints, 241 are dihedral angle restraints, 74 are distance restraints derived from putative ...Details: The structures are based on a total of 2961 restraints: 2553 are NOE-derived distance constraints, 241 are dihedral angle restraints, 74 are distance restraints derived from putative hydrogen bonds, and 93 are angle restraints based on residual dipolar couplings
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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