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- PDB-1kcy: NMR solution structure of apo calbindin D9k (F36G + P43M mutant) -

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Basic information

Entry
Database: PDB / ID: 1kcy
TitleNMR solution structure of apo calbindin D9k (F36G + P43M mutant)
Componentscalbindin D9k
KeywordsMETAL BINDING PROTEIN / EF HAND / CALCIUM-BINDING PROTEIN / STRUCTURE PERTURBING MUTATION / FOUR HELIX BUNDLE
Function / homology
Function and homology information


vitamin D binding / calcium-dependent protein binding / collagen-containing extracellular matrix / 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 / 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 / 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
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsNelson, M.R. / Thulin, E. / Fagan, P.A. / Forsen, S. / Chazin, W.J.
CitationJournal: Protein Sci. / Year: 2002
Title: The EF-hand domain: a globally cooperative structural unit.
Authors: Nelson, M.R. / Thulin, E. / Fagan, P.A. / Forsen, S. / Chazin, W.J.
History
DepositionNov 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: 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_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE P43M is the background mutation used in the Chazin lab to study all calbindin D9k mutants. ...SEQUENCE P43M is the background mutation used in the Chazin lab to study all calbindin D9k mutants. This mutation removes spectra-complicating cis-trans isomerization at Pro43 but does not otherwise affect the structure.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: calbindin D9k


Theoretical massNumber of molelcules
Total (without water)8,4551
Polymers8,4551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 50The full ensemble was ordered by lowest residual constraint violations, then the top 22 with favorable covalent geometries and AMBER energies were selected
RepresentativeModel #1closest to the average

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Components

#1: Protein calbindin D9k / CABP / Vitamin D-dependent calcium-binding protein / intestinal


Mass: 8454.515 Da / Num. of mol.: 1
Fragment: contains EF-HAND 1 (LOW AFFINITY) and EF-HAND 2 (HIGH AFFINITY)
Mutation: F36G, P43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pRCB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P02633

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D COSY
1212D NOESY
1312D TOCSY
1432D NOESY
1522D 15N-1H HSQC
1623D 15N-separated TOCSY
1723D 15N-separated NOESY
182HNHA
192HNHB
NMR detailsText: This structure was determined using a combination of standard 2D homonuclear and 15N-based 3D methods.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM calbindin; 95% H2O; 5% D2O95% H20; 5% D2O
22.5 mM calbindin D9k U-15N; 95% H2O; 5% D2O95% H2O/5% D2O
32.5 mM calbindin D9k; 100% D20100% D2O
Sample conditionsIonic strength: no added salts / pH: 6.0 / Pressure: ambient / Temperature: 300 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
DIANA2.8Guntertstructure solution
Amber4.1Pearlmannstructure solution
Felix97Molecular Simulations, Inc.data analysis
GLOMSAunknownGuntertdata analysis
GENXPK1Gippertdata analysis
Amber4.1Pearlmannrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on 1042 NOE restraints (186 intraresidue, 269 sequential, 289 medium range (2-4 residues apart), 298 long range), 18 hydrogen bond restraints (assigned as described ...Details: The structures are based on 1042 NOE restraints (186 intraresidue, 269 sequential, 289 medium range (2-4 residues apart), 298 long range), 18 hydrogen bond restraints (assigned as described in Skelton et al., 1995), and 115 dihedral constraints (45 phi, 42 psi, and 28 chi1).
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The full ensemble was ordered by lowest residual constraint violations, then the top 22 with favorable covalent geometries and AMBER energies were selected
Conformers calculated total number: 50 / Conformers submitted total number: 22

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