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- PDB-1jwd: Ca2+-induced Structural Changes in Calcyclin: High-resolution Sol... -

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Basic information

Entry
Database: PDB / ID: 1jwd
TitleCa2+-induced Structural Changes in Calcyclin: High-resolution Solution Structure of Ca2+-bound Calcyclin.
ComponentsCalcyclin
KeywordsMETAL BINDING PROTEIN / Ca(2+)-binding protein / S100 protein / EF-hand / S100A6
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, restrained molecular dynamics
AuthorsMaler, L. / Sastry, M. / Chazin, W.J.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: A structural basis for S100 protein specificity derived from comparative analysis of apo and Ca(2+)-calcyclin
Authors: Maler, L. / Sastry, M. / Chazin, W.J.
#1: 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.M. / Chazin, W.J.
#2: Journal: Structure / Year: 1998
Title: The Three-dimenisonal 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.
#3: 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. / Chase, D.A. / Chazin, W.J.
History
DepositionSep 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / 100The program Findfam was used to establish that the number of structures required to accurately represent the ensemble was less than 22 (the number selected to represent previous S100A6 ensembles). Structures were ordered by lowest restraint violations, then accepted if total molecular energy and each contributing term was within two standard deviations of the mean. The 22 structures with least restraint violations (energy penalty and magnitude of largest violation) all met these criteria.
RepresentativeModel #1closest to the average

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Components

#1: Protein Calcyclin / Lung 10 kDa Protein


Mass: 10167.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: R-S100A6 / Organ: LUNG / Plasmid: PET1120 / 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 13C-separated NOESY
1323D 15N-separated NOESY
1423D HACAHB
1533D 13C-filter,13C-edited NOESY
1643D 15N-separated NOESY
1752D 13C HSQC
NMR detailsText: Dimer constraints were obtained from the 3D_13C-filter,13C-edited experiment in combination with 3D_13C-separated_NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM calcyclin, 50 MM TRIS buffer, 30 mM CaCl290% H2O/10% D2O
22 mM 15N, 13C-enriched calcyclin, 50 mM TRIS-buffer, 0.05% NaN3, 30 mM CaCl290% H2O/10% D2O
31:1 15N,13C-enriched:unlabled calcyclin, 50 mM TRIS-buffer, 0.05% NaN3, 30 mM CaCl290% H2O/10% D2O
415N-enriched calcyclin, 50 mM TRIS-buffer, 0.05% NaN3, 30 mM CaCl290% H2O/10% D2O
510% 13C-enriched calcyclin, 50 mM TRIS-buffer, 0.05% NaN3, 30 mM CaCl2D2O
Sample conditionsIonic strength: 30 mM CaCl2 / pH: 7.0 / 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 DMXBrukerDMX7501
Bruker DRXBrukerDRX6002
Bruker AMXBrukerAMX5003

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Processing

NMR software
NameVersionDeveloperClassification
Felix97MSIdata analysis
DIANA2.8Guntert, Braun & Wuthrichstructure solution
Amber4.1Pearlmann, Case, Caldwell, Ross, Cheatham III, Ferguson, Seibel, Singh, Weiner & Kollmanrefinement
FINDFAM1Smith, Chazin & Casedata analysis
RefinementMethod: distance geometry, restrained molecular dynamics / Software ordinal: 1
Details: The calculations were carried out using a total of 3104 distance and 294 torsion angle constraints. Starting structures were generated as monomers (one chain) with no intersubunit ...Details: The calculations were carried out using a total of 3104 distance and 294 torsion angle constraints. Starting structures were generated as monomers (one chain) with no intersubunit constraints using distance geometry followed by restrained molecular dynamics (rMD). The dimer structures were generated by rMD docking driven by the intersubunit NOEs using two arbitrarily selected starting subunit structures. Each dimer was further refined by rMD with all constraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The program Findfam was used to establish that the number of structures required to accurately represent the ensemble was less than 22 (the number selected to represent ...Conformer selection criteria: The program Findfam was used to establish that the number of structures required to accurately represent the ensemble was less than 22 (the number selected to represent previous S100A6 ensembles). Structures were ordered by lowest restraint violations, then accepted if total molecular energy and each contributing term was within two standard deviations of the mean. The 22 structures with least restraint violations (energy penalty and magnitude of largest violation) all met these criteria.
Conformers calculated total number: 100 / Conformers submitted total number: 22

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