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- PDB-1rt0: 12-mer from site II calbindin D9K (DKNGDGEVSFEE) coordinating Zn(II) -

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Basic information

Entry
Database: PDB / ID: 1rt0
Title12-mer from site II calbindin D9K (DKNGDGEVSFEE) coordinating Zn(II)
ComponentsVitamin D-dependent calcium-binding protein, intestinal
KeywordsMETAL BINDING PROTEIN / EF-hand toxic metal ion transport model of ICaBP coordination toward zinc
Function / homology
Function and homology information


vitamin D binding / calcium-dependent protein binding / calcium ion binding / extracellular space / cytoplasm
Similarity search - Function
S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / 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
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFerrari, R. / Mendoza, G. / James, T. / Tonelli, M. / Basus, V. / Gasque, L.
CitationJournal: To be Published
Title: Coordination Compounds derived from a dodecapeptide and Pb2+, Cd2+ and Zn2+. Modeling the site II from the Calbindin D9K
Authors: Ferrari, R. / Mendoza, G. / James, T. / Tonelli, M. / Basus, V. / Gasque, L.
History
DepositionDec 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Vitamin D-dependent calcium-binding protein, intestinal


Theoretical massNumber of molelcules
Total (without water)1,3261
Polymers1,3261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Vitamin D-dependent calcium-binding protein, intestinal / CABP / Calbindin D9K


Mass: 1326.301 Da / Num. of mol.: 1 / Fragment: residues 57-68 (SWS P02632) / Source method: obtained synthetically
Details: Occurs naturaly in mammals calcium binding protein as the second calcium binding site. Purchased to Commonwealth Biotechnologies, Inc. as the trifluoroacetate salt, pur. min 95%
References: UniProt: P02633

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121noesyjr

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Sample preparation

DetailsContents: 3mM Peptide and Zn(NO3)2. NaOH and HNO3 added for pH fixing to 7; 80% H2O, 20% D2O
Solvent system: 80% H2O, 20% D2O
Sample conditionsIonic strength: aprox 0 / pH: 7 / Pressure: ambient / Temperature: 288 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer, A. Baxprocessing
MARDIGRAS3.2James, Borgias, Thomas, Liu, Kumar, Tonelliiterative matrix relaxation
DYANA1.5Guenter, Mumenthaler, Herrmannstructure solution
DYANA1.5Guenter, Mumenthaler, Herrmannrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: after a matrix relaxation
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 10

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