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- PDB-1snl: NMR Solution Structure of the Calcium-binding Domain of Nucleobin... -

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Basic information

Entry
Database: PDB / ID: 1snl
TitleNMR Solution Structure of the Calcium-binding Domain of Nucleobindin (CALNUC)
ComponentsNucleobindin 1
KeywordsMETAL BINDING PROTEIN / EF-HAND / CALCIUM-BINDING
Function / homology
Function and homology information


extrinsic component of Golgi membrane / lumenal side of Golgi membrane / response to cisplatin / regulation of protein targeting / protein metabolic process => GO:0019538 / cis-Golgi network / Golgi-associated vesicle / Golgi cisterna membrane / small GTPase-mediated signal transduction / endoplasmic reticulum-Golgi intermediate compartment ...extrinsic component of Golgi membrane / lumenal side of Golgi membrane / response to cisplatin / regulation of protein targeting / protein metabolic process => GO:0019538 / cis-Golgi network / Golgi-associated vesicle / Golgi cisterna membrane / small GTPase-mediated signal transduction / endoplasmic reticulum-Golgi intermediate compartment / G-protein alpha-subunit binding / rough endoplasmic reticulum / guanyl-nucleotide exchange factor activity / post-translational protein modification / Post-translational protein phosphorylation / trans-Golgi network / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / early endosome / endoplasmic reticulum lumen / calcium ion binding / DNA binding / extracellular space / extracellular exosome / membrane / nucleus
Similarity search - Function
Nucleobindin / Nucleobindin-1 / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...Nucleobindin / Nucleobindin-1 / EF-hand / Recoverin; domain 1 / EF-hand domain pair / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
Authorsde Alba, E. / Tjandra, N.
CitationJournal: Biochemistry / Year: 2004
Title: Structural Studies on the Ca(2+)-binding Domain of Human Nucleobindin (Calnuc).
Authors: De Alba, E. / Tjandra, N.
History
DepositionMar 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleobindin 1


Theoretical massNumber of molelcules
Total (without water)12,4201
Polymers12,4201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nucleobindin 1 / / CALNUC


Mass: 12419.804 Da / Num. of mol.: 1 / Fragment: calcium-binding domain
Source method: isolated from a genetically manipulated source
Details: contains EF-hand 1 and EF-hand 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: NUCB1, NUC / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON PLUS RP / References: UniProt: Q02818

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC, 3D-15N separated-NOESY
1224D-15N,13C separated NOESY, HNCO, CBCA(CO)NH, HN(CA)CB, HCONHCCONH
1334D-13C,13C separated NOESY,(H)CCH-TOCSY
144HNCO, HCACONH, 13C-HSQC JMOD

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Ca-binding domain of nucleobindin, U-15N, 5mM CaCl2, 0.1mM NaN3, pH 6.890% H2O/10% D2O
21mM Ca-binding domain of nucleobindin, U-15N,U-13C, 5mM CaCl2, 0.1mM NaN3, pH 6.890% H2O/10% D2O
31mM Ca-binding domain of nucleobindin, U-15N,U-13C, 5mM CaCl2, 0.1mM NaN3, pH 6.8100% D2O
40.7mM Ca-binding domain of nucleobindin, U-15N,U-13C, 5mM CaCl2, 0.1mM NaN3, pH 6.890% H2O, 10% D2O, Pf1 bacteriophage
Sample conditionsIonic strength: 5 mM CaCl2, 0.1 mM NaN3, 5mM KCl / pH: 6.8 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR2.5Brukercollection
XwinNMR2.5Brukerdata analysis
NMRPipe2.1Delaglio, F.processing
PIPP4.2.8Garrett, D.data analysis
XPLOR-NIH2.9.3Schwieters, kuszewski, Tjandra, Clorerefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: Residual dipolar couplings used for structure refinement. Residues 1-17, 47-63, 95-99 are flexible and were not considered in the superposition of the 20 structures.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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