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- PDB-1a03: THE THREE-DIMENSIONAL STRUCTURE OF CA2+-BOUND CALCYCLIN: IMPLICAT... -

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Entry
Database: PDB / ID: 1a03
TitleTHE THREE-DIMENSIONAL STRUCTURE OF CA2+-BOUND CALCYCLIN: IMPLICATIONS FOR CA2+-SIGNAL TRANSDUCTION BY S100 PROTEINS, NMR, 20 STRUCTURES
ComponentsCALCYCLIN (RABBIT, CA2+)
KeywordsCALCIUM-BINDING PROTEIN / EF-HAND / S-100 PROTEIN
Function / homology
Function and homology information


S100 protein binding / cytoplasmic side of plasma membrane / calcium-dependent protein binding / nuclear envelope / calcium ion binding / perinuclear region of cytoplasm / extracellular space / cytosol
Similarity search - Function
Protein S100-A6 / 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 / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...Protein S100-A6 / 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 / 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 speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / METRIC MATRIX DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING
AuthorsSastry, M. / Ketchem, R.R. / Crescenzi, O. / Weber, C. / Lubienski, M.J. / Hidaka, H. / Chazin, W.J.
Citation
Journal: Structure / Year: 1998
Title: The three-dimensional structure of Ca(2+)-bound calcyclin: implications for Ca(2+)-signal transduction by S100 proteins.
Authors: Sastry, M. / Ketchem, R.R. / Crescenzi, O. / Weber, C. / Lubienski, M.J. / Hidaka, H. / Chazin, W.J.
#1: Journal: Protein Sci. / Year: 1996
Title: 1H NMR Assignments of Apo Calcyclin and Comparative Structural Analysis with Calbindin D9K and S100 Beta
Authors: Potts, B.C. / Carlstrom, G. / Okazaki, K. / Hidaka, H. / Chazin, W.J.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: The Structure of Calcyclin Reveals a Novel Homodimeric Fold for S100 Ca(2+)-Binding Proteins
Authors: Potts, B.C. / Smith, J. / Akke, M. / Macke, T.J. / Okazaki, K. / Hidaka, H. / Case, D.A. / Chazin, W.J.
#3: Journal: Nat.Struct.Biol. / Year: 1995
Title: Erratum. The Structure of Calcyclin Reveals a Novel Homodimeric Fold for S100 Ca(2+)-Binding Proteins
Authors: Potts, B.C. / Smith, J. / Akke, M. / Macke, T.J. / Okazaki, K. / Hidaka, H. / Case, D.A. / Chazin, W.J.
#4: Journal: Arch.Biochem.Biophys. / Year: 1991
Title: A Calcium-Binding Protein from Rabbit Lung Cytosol Identified as the Product of Growth-Regulated Gene (2A9) and its Binding Proteins
Authors: Tokumitsu, H. / Kobayashi, R. / Hidaka, H.
#5: Journal: Arch.Biochem.Biophys. / Year: 1991
Title: Erratum. A Calcium-Binding Protein from Rabbit Lung Cytosol Identified as the Product of Growth-Regulated Gene (2A9) and its Binding Proteins
Authors: Tokumitsu, H. / Kobayashi, R. / Hidaka, H.
History
DepositionDec 8, 1997Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: 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
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
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: CALCYCLIN (RABBIT, CA2+)
B: CALCYCLIN (RABBIT, CA2+)


Theoretical massNumber of molelcules
Total (without water)20,3352
Polymers20,3352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 192LEAST RESTRAINT VIOLATION ENERGY
RepresentativeModel #1

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Components

#1: Protein CALCYCLIN (RABBIT, CA2+) / 2A9 / CACY / S100A6 / PRA


Mass: 10167.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RABBIT, CA2+ / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line: BL21 / Gene: R-S100A6 / Organ: LUNG / Plasmid: PET1120 / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Gene (production host): R-S100A6 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P30801

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE MANUSCRIPT

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Sample preparation

DetailsContents: 95% H2O, 5% D2O
Sample conditionsIonic strength: 50mM TRIS, 20-38mM CACL2 / pH: 7 / Temperature: 300 K
Crystal grow
*PLUS
Method: other

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DMXBrukerDMX7502
Bruker DRXBrukerDRX7503

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Processing

NMR software
NameVersionDeveloperClassification
SPEARLMAN,CArefinement
DISGEOstructure solution
Amber4.1structure solution
RefinementMethod: METRIC MATRIX DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING
Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION ENERGY
Conformers calculated total number: 192 / Conformers submitted total number: 20

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