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- PDB-2ksz: The solution structure of the Magnesium bound soybean calmodulin ... -

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Basic information

Entry
Database: PDB / ID: 2ksz
TitleThe solution structure of the Magnesium bound soybean calmodulin isoform 4 N-domain
ComponentsPutative uncharacterized protein
KeywordsMETAL BINDING PROTEIN / soybean calmodulin isoform 4 / Magnesium / Residual Dipolar Coupling
Function / homology
Function and homology information


enzyme regulator activity / calcium ion binding
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest RDC energy, model 1
AuthorsHuang, H. / Ishida, H. / Vogel, H.J.
CitationJournal: Protein Sci. / Year: 2010
Title: The solution structure of the Mg2+ form of soybean calmodulin isoform 4 reveals unique features of plant calmodulins in resting cells.
Authors: Huang, H. / Ishida, H. / Vogel, H.J.
History
DepositionJan 14, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 10, 2014Group: Structure summary
Revision 1.3May 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.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

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4833
Polymers8,4341
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 10structures with the lowest RDC energy
RepresentativeModel #1lowest rdc energy

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Components

#1: Protein Putative uncharacterized protein / sCaM4-NT / Calmodulin


Mass: 8434.247 Da / Num. of mol.: 1 / Fragment: sCaM4 N-terminal domain
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 15N-HSQC-IPAP
1223D IPAP-J-HNCO(CA)-CaHa RDC
1323D IPAP-J-HNCO-CaCO RDC
1413D HN(CA)CB
1513D HNCO
1613D HN(CO)CA
1713D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] Mg-sCaM4-1, 20 mM MAGNESIUM ION-2, 100 mM potassium chloride-3, 0.5 mM EGTA-4, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] Mg-sCaM4-5, 20 mM MAGNESIUM ION-6, 100 mM potassium chloride-7, 0.5 mM EGTA-8, 16 mg/mL Pf1 phage-9, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-100% 15N] Mg-sCaM4-10, 20 mM MAGNESIUM ION-11, 100 mM potassium chloride-12, 0.5 mM EGTA-13, 16 mg/mL Pf1 phage-14, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMg-sCaM4-1[U-100% 13C; U-100% 15N]1
20 mMMAGNESIUM ION-21
100 mMpotassium chloride-31
0.5 mMEGTA-41
0.5 mMMg-sCaM4-5[U-100% 13C; U-100% 15N]2
20 mMMAGNESIUM ION-62
100 mMpotassium chloride-72
0.5 mMEGTA-82
16 mg/mLPf1 phage-92
0.5 mMMg-sCaM4-10[U-100% 15N]3
20 mMMAGNESIUM ION-113
100 mMpotassium chloride-123
0.5 mMEGTA-133
16 mg/mLPf1 phage-143
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest rdc energy
NMR ensembleConformer selection criteria: structures with the lowest RDC energy
Conformers calculated total number: 10 / Conformers submitted total number: 5 / Representative conformer: 1

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