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- PDB-1nya: NMR SOLUTION STRUCTURE OF CALERYTHRIN, AN EF-HAND CALCIUM-BINDING... -

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Entry
Database: PDB / ID: 1nya
TitleNMR SOLUTION STRUCTURE OF CALERYTHRIN, AN EF-HAND CALCIUM-BINDING PROTEIN
ComponentsCalerythrin
KeywordsMETAL BINDING PROTEIN / EF-hand
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
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 speciesSaccharopolyspora erythraea (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTossavainen, H. / Permi, P. / Annila, A. / Kilpelainen, I. / Drakenberg, T.
Citation
Journal: Eur.J.Biochem. / Year: 2003
Title: NMR solution structure of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea
Authors: Tossavainen, H. / Permi, P. / Annila, A. / Kilpelainen, I. / Drakenberg, T.
#1: Journal: Protein Sci. / Year: 1999
Title: NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea
Authors: Aitio, H. / Annila, A. / Heikkinen, S. / Thulin, E. / Drakenberg, T. / Kilpelainen, I.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / 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_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Calerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1784
Polymers19,0581
Non-polymers1203
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 225structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calerythrin / Calcium-binding protein


Mass: 19058.025 Da / Num. of mol.: 1 / Mutation: T108I,W109V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P06495
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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 13C-separated NOESY
1213D 15N-separated NOESY
232a/b-TROSY
242HNCO(a/b-COCA-J)
252HN(a/b-NCO-J)-TROSY
262a/b-HN(CO)CA-J

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM calerythrin U-15N,13C4mM CaCl, 5mM DTT, 2mM NaN3, 95% H2O, 5% D2O
21mM calerythrin U-15N,13C4mM CaCl, 5mM DTT, 2mM NaN3, 20mM bisTris, 90% H2O, 10% D2O, 30 mg/ml Pf1 phage
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.0 ambient 318 K
26.0 ambient 318 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
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVarian inccollection
Felix97MSI/Accelrysdata analysis
Sparky3.1Goddard and Knellerdata analysis
NMRPipe2.2Delaglio et al.processing
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 225 / Conformers submitted total number: 20

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