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- PDB-2cnp: HIGH RESOLUTION SOLUTION STRUCTURE OF APO RABBIT CALCYCLIN, NMR, ... -

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Basic information

Entry
Database: PDB / ID: 2cnp
TitleHIGH RESOLUTION SOLUTION STRUCTURE OF APO RABBIT CALCYCLIN, NMR, 22 STRUCTURES
ComponentsCALCYCLIN
KeywordsCALCIUM-BINDING PROTEIN / EF-HAND / S-100 PROTEIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


S100 protein binding / cytoplasmic side of plasma membrane / calcium-dependent protein binding / nuclear envelope / collagen-containing extracellular matrix / 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 / DISTANCE GEOMETRY VARIABLE TARGET FUNCTION ALGORITHM, RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING
AuthorsMaler, L. / Potts, B.C.M. / Chazin, W.J.
Citation
Journal: J.Biomol.NMR / Year: 1999
Title: High resolution solution structure of apo calcyclin and structural variations in the S100 family of calcium-binding proteins.
Authors: Maler, L. / Potts, B.C. / 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: 1995
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.
History
DepositionJan 7, 1999Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
B: CALCYCLIN


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)22 / 112DEFINED THE MINIMAL NUMBER OF CONFORMERS NEEDED TO REPRESENT THE SRUCTURE. THE MEMBERS OF THE ENSEMBLE WERE CHOSEN BASED ON A COMBINATION OF LEAST RESTRAINT VIOLATION ENERGY AND MOLECULAR ENERGIES.
RepresentativeModel #1

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Components

#1: Protein CALCYCLIN / 2A9 / CACY / S100A6 / PRA


Mass: 10167.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Organ: LUNG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30801

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D/4D NOESY
121SEE MANUSCRIPT.
NMR detailsText: CHEMICAL SHIFT ASSIGNMENTS WERE MADE BASED ON TRIPLE-RESONANCE EXPERIMENTS. DISTANCE CONTRAINTS WERE GENERATED FROM 2D HOMONUCLEAR NOESY, 3D 13C-NOESY-HSQC, 4D 13C/13C-NOESY-HMQC-NOESY, 2D AND ...Text: CHEMICAL SHIFT ASSIGNMENTS WERE MADE BASED ON TRIPLE-RESONANCE EXPERIMENTS. DISTANCE CONTRAINTS WERE GENERATED FROM 2D HOMONUCLEAR NOESY, 3D 13C-NOESY-HSQC, 4D 13C/13C-NOESY-HMQC-NOESY, 2D AND 3D 13C-SELECT, 13C-FILTERED NOESY. TORSION ANGLE CONSTRAINTS WERE GENERATED FROM HACAHB-COSY, HNHA, HSQC AND NOESY EXPERIMENTS.

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Sample preparation

Sample conditionspH: 7 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DIANAstructure solution
Amber4.1structure solution
RefinementMethod: DISTANCE GEOMETRY VARIABLE TARGET FUNCTION ALGORITHM, RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING
Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING DIANA, FOLLOWED BY RESTRAINED MOLECULAR DYNAMICS ANNEALING EMPLOYING THE FULL AMBER 4.1 FORCE FIELD TO CREATE MONOMER STRUCTURES. THE DIMER WAS CREATED ...Details: THE STRUCTURES WERE CALCULATED USING DIANA, FOLLOWED BY RESTRAINED MOLECULAR DYNAMICS ANNEALING EMPLOYING THE FULL AMBER 4.1 FORCE FIELD TO CREATE MONOMER STRUCTURES. THE DIMER WAS CREATED BY DOCKING TWO COPIES OF A MONOMER AND FURTHER ANNEALING, ALL USING RESTRAINED MOLECULAR DYNAMICS.
NMR ensembleConformer selection criteria: DEFINED THE MINIMAL NUMBER OF CONFORMERS NEEDED TO REPRESENT THE SRUCTURE. THE MEMBERS OF THE ENSEMBLE WERE CHOSEN BASED ON A COMBINATION OF LEAST RESTRAINT VIOLATION ...Conformer selection criteria: DEFINED THE MINIMAL NUMBER OF CONFORMERS NEEDED TO REPRESENT THE SRUCTURE. THE MEMBERS OF THE ENSEMBLE WERE CHOSEN BASED ON A COMBINATION OF LEAST RESTRAINT VIOLATION ENERGY AND MOLECULAR ENERGIES.
Conformers calculated total number: 112 / Conformers submitted total number: 22

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