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- PDB-1cdn: Solution structure of (CD2+)1-calbindin D9K reveals details of th... -

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Entry
Database: PDB / ID: 1cdn
TitleSolution structure of (CD2+)1-calbindin D9K reveals details of the stepwise structural changes along the apo--> (CA2+)II1--> (CA2+)I,II2 binding pathway
ComponentsCALBINDIN D9K
KeywordsCALCIUM-BINDING PROTEIN / EF-HAND
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
AuthorsAkke, M. / Forsen, S. / Chazin, W.J.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Solution structure of (Cd2+)1-calbindin D9k reveals details of the stepwise structural changes along the Apo-->(Ca2+)II1-->(Ca2+)I,II2 binding pathway.
Authors: Akke, M. / Forsen, S. / Chazin, W.J.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Determination of the Solution Structure of Apo Calbindin D9K by NMR Spectroscopy
Authors: Skelton, N.J. / Koerdel, J. / Chazin, W.J.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: High-Resolution Solution Structure of Calcium-Loaded Calbindin D9K
Authors: Kordel, J. / Skelton, N.J. / Akke, M. / Chazin, W.J.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Molecular Basis for Co-Operativity in Ca2+ Binding in Calbindin D9K. 1H Nuclear Magnetic Resonance Studies of (Cd2+)1-Bovine Calbindin D9K
Authors: Akke, M. / Forsen, S. / Chazin, W.J.
History
DepositionAug 4, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_nmr_software.name / _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: CALBINDIN D9K


Theoretical massNumber of molelcules
Total (without water)8,6021
Polymers8,6021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / -
Representative

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Components

#1: Protein CALBINDIN D9K / INTESTINAL CALCIUM-BINDING PROTEIN / ICBP / ICABP / CABP9K / S100D


Mass: 8601.688 Da / Num. of mol.: 1 / Mutation: INS(MET 1), P43G
Source method: isolated from a genetically manipulated source
Details: BOVINE MINOR A FORM, CADMIUM-HALF-SATURATED, CADMIUM ION IS BOUND IN C-TERMINAL SITE
Source: (gene. exp.) Bos taurus (cattle) / Gene: ICABP / Plasmid: PICB1 / Gene (production host): ICABP / Production host: Escherichia coli (E. coli) / References: UniProt: P02633

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameVersionDeveloperClassification
DISGEOHAVEL,WUTHRICHrefinement
Amber4PEARLMAN,CASE,CALDWELL,SEIBEL,SINGH,WEINER,KOLLMANrefinement
NMR ensembleConformers submitted total number: 24

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