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- PDB-1n65: FAMILY OF NMR SOLUTION STRUCTURES OF CA CE CALBINDIN D9K IN DENAT... -

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Basic information

Entry
Database: PDB / ID: 1n65
TitleFAMILY OF NMR SOLUTION STRUCTURES OF CA CE CALBINDIN D9K IN DENATURATING CONDITIONS
ComponentsVitamin D-dependent calcium-binding protein, intestinal
KeywordsMETAL BINDING PROTEIN / CALCIUM BINDING PROTEINS / NMR SOLUTION STRUCTURE / PARAMAGNETISM-BASED CONSTRAINTS / DENATURATING AGENTS / GUANIDINIUM CHLORIDE
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
CERIUM (III) ION / Protein S100-G
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / TAD Simulated annealing
AuthorsJimenez, B. / Poggi, L. / Piccioli, M.
CitationJournal: Biochemistry / Year: 2003
Title: Monitoring the Early Steps of Unfolding of Dicalcium and Mono-Ce(3+)-Substituted Forms of P43M Calbindin D(9k).
Authors: Jimenez, B. / Poggi, L. / Piccioli, M.
History
DepositionNov 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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, intestinal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6852
Polymers8,5451
Non-polymers1401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1closest to the average

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Components

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


Mass: 8544.637 Da / Num. of mol.: 1 / Mutation: P43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CALB3 OR S100D / Production host: Escherichia coli (E. coli) / References: UniProt: P02633
#2: Chemical ChemComp-CE / CERIUM (III) ION


Mass: 140.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ce

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N HSQC
2223D 15N-separated NOESY
NMR detailsText: NOESY constraints were obtained on the native form of the protein, while paramagnetic constraints were collected in the presence of 2M Guanidinium Chloride

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Sample preparation

Details
Solution-IDContentsSolvent system
1Uniform labeling with 15N, H2O/D20 90/10H2O/D20 90/10 Denaturating Conditions
2Uniform labeling with 15N, H2O/D20 90/10H2O/D20 90/10
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
12M Guanidinium Chloride (GmdHCl) 6.0 1 atm298 K
2pure water 6.0 1 atm298 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 AVANCEBrukerAVANCE8001
Bruker DMXBrukerDMX5002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE6004
Bruker AVANCEBrukerAVANCE4005

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Processing

NMR software
NameVersionDeveloperClassification
PARAMAGNETIC-DYANA1Barbieri R., Bertini I., Cavallaro G., Lee Y.-M., Luchinat C., Rosato A.structure solution
PSEUDYANA3.1L.BANCI,I.BERTINI,M.A.CREMONINI,G.GORI SAVELLINI,C.LUCHINAT,K.WUTHRICH AND P.GUNTERTrefinement
RefinementMethod: TAD Simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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