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- PDB-1ksm: AVERAGE NMR SOLUTION STRUCTURE OF CA LN CALBINDIN D9K -

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Basic information

Entry
Database: PDB / ID: 1ksm
TitleAVERAGE NMR SOLUTION STRUCTURE OF CA LN CALBINDIN D9K
ComponentsVITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / LANTHANIDE IONS / CALCIUM-BINDING PROTEIN / PARAMAGNETIC NMR / PSEUDOCONTACT SHIFTS / RESIDUAL DIPOLAR COUPLINGS
Function / homology
Function and homology information


vitamin D binding / calcium-dependent protein binding / basolateral plasma membrane / apical plasma membrane / calcium ion binding / 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 domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...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 domain / EF-hand / Recoverin; domain 1 / 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
LANTHANUM (III) ION / Protein S100-G
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / SIMULATED ANNEALING TORSION ANGLE DYNAMICS
Model type detailsminimized average
AuthorsBertini, I. / Donaire, A. / Luchinat, C. / Piccioli, M. / Poggi, L. / Parigi, G. / Jimenez, B.
CitationJournal: J.Biomol.NMR / Year: 2001
Title: Paramagnetism-based versus classical constraints: an analysis of the solution structure of Ca Ln calbindin D9k.
Authors: Bertini, I. / Donaire, A. / Jimenez, B. / Luchinat, C. / Parigi, G. / Piccioli, M. / Poggi, L.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJan 23, 2002ID: 1K31
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: VITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1022
Polymers8,9631
Non-polymers1391
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 30minimized average structure
RepresentativeModel #1minimized average structure

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Components

#1: Protein VITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN / CABP / CALBINDIN D9K


Mass: 8963.168 Da / Num. of mol.: 1 / Mutation: P43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P02633
#2: Chemical ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: La

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
121HNHA
131RELAXATION RATES
141J -MODULATED HSQC
151HNCO
161HNCA
171(H)CCH-TOCSY

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Sample preparation

DetailsContents: 1.5 MM [15N, 13C] - CA LN CALBINDIN, PH 6.0 / Solvent system: H20:D2O 90:10
Sample conditionsIonic strength: WATER SOLUTION / pH: 6 / Pressure: AMBIENT / Temperature: 300.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, P., Mumenthaler, C. and Wuethrich, Kstructure solution
PSEUDYANA1.5Banci, L., Bertini, I., Cremonini, M.A., Gori Savellini, G., Luchinat, C., Wuthrich, K. and Guntert, P.structure solution
PSEUDYANA3.1Banci, L., Bertini, I., Cremonini, M.A., Gori Savellini, G., Luchinat, C., Wuthrich, K. and Guntert, P.refinement
RefinementMethod: SIMULATED ANNEALING TORSION ANGLE DYNAMICS / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: minimized average structure / Conformers calculated total number: 30 / Conformers submitted total number: 1

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