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- PDB-2l1w: The solution structure of soybean calmodulin isoform 4 complexed ... -

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Basic information

Entry
Database: PDB / ID: 2l1w
TitleThe solution structure of soybean calmodulin isoform 4 complexed with the vacuolar calcium ATPase BCA1 peptide
Components
  • Calmodulin
  • vacuolar calcium ATPase BCA1 peptide
KeywordsMETAL BINDING PROTEIN / Calmodulin / Calmodulin complex / Soybean calmodulin / Vacuolar calcium ATPase
Function / homology
Function and homology information


enzyme regulator activity / calcium ion binding
Similarity search - Function
EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / 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 ...EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / 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 speciesGlycine max (soybean)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsIshida, H. / Vogel, H.J.
CitationJournal: To be Published
Title: The solution structure of a plant calmodulin and the CaM-binding domain of the vacuolar calcium-ATPase BCA1 reveals a new binding and activation mechanism
Authors: Ishida, H. / Vogel, H.
History
DepositionAug 6, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: vacuolar calcium ATPase BCA1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1596
Polymers19,9982
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin


Mass: 16901.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: SCaM-4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39890
#2: Protein/peptide vacuolar calcium ATPase BCA1 peptide


Mass: 3096.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CA)CO
1513D H(CCO)NH
1613D HBHA(CO)NH
1713D C(CO)NH
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11143D 13C/F3-filter 13C/F1-edited NOESY
11232D 13C,15N-filter NOESY
11342D 13C-fliter COSY
2145IPAP-1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.300 mM [U-98% 13C; U-98% 15N] protein_1-1, 0.375 mM protein_2-2, 5 mM CALCIUM ION-3, 100 mM potassium chloride-4, 10 mM DTT-5, 90% H2O/10% D2O90% H2O/10% D2O
20.300 mM [U-98% 13C; U-98% 15N] protein_1-6, 0.375 mM protein_2-7, 5 mM CALCIUM ION-8, 100 mM potassium chloride-9, 10 mM DTT-10, 100% D2O100% D2O
30.300 mM [U-98% 13C; U-98% 15N] protein_1-11, 0.255 mM protein_2-12, 5 mM CALCIUM ION-13, 100 mM potassium chloride-14, 10 mM DTT-15, 90% H2O/10% D2O90% H2O/10% D2O
40.300 mM [U-98% 13C; U-98% 15N] protein_1-16, 0.255 mM protein_2-17, 5 mM CALCIUM ION-18, 100 mM potassium chloride-19, 10 mM DTT-20, 100% D2O100% D2O
50.300 mM [U-98% 15N] protein_1-21, 0.375 mM protein_2-22, 5 mM CALCIUM ION-23, 300 mM potassium chloride-24, 10 mM DTT-25, 16 mg/ml Pf1 phage-26, 20 mM bis-Tris-27, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.300 mMprotein_1-1[U-98% 13C; U-98% 15N]1
0.375 mMprotein_2-21
5 mMCALCIUM ION-31
100 mMpotassium chloride-41
10 mMDTT-51
0.300 mMprotein_1-6[U-98% 13C; U-98% 15N]2
0.375 mMprotein_2-72
5 mMCALCIUM ION-82
100 mMpotassium chloride-92
10 mMDTT-102
0.300 mMprotein_1-11[U-98% 13C; U-98% 15N]3
0.255 mMprotein_2-123
5 mMCALCIUM ION-133
100 mMpotassium chloride-143
10 mMDTT-153
0.300 mMprotein_1-16[U-98% 13C; U-98% 15N]4
0.255 mMprotein_2-174
5 mMCALCIUM ION-184
100 mMpotassium chloride-194
10 mMDTT-204
0.300 mMprotein_1-21[U-98% 15N]5
0.375 mMprotein_2-225
5 mMCALCIUM ION-235
300 mMpotassium chloride-245
10 mMDTT-255
16 mg/mLPf1 phage-265
20 mMbis-Tris-275
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 7 ambient 303 K
20.3 7 ambient 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25 / Representative conformer: 1

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