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- PDB-4bya: Calmodulin, C-terminal domain, M144H mutant -

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Basic information

Entry
Database: PDB / ID: 4bya
TitleCalmodulin, C-terminal domain, M144H mutant
ComponentsCALMODULIN, C-TERMINAL DOMAIN, M144H MUTANT
KeywordsMETAL BINDING PROTEIN / CALMODULIN
Function / homology
Function and homology information


CH domain binding / myosin binding / disordered domain specific binding / calcium ion binding / protein-containing complex
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 speciesGALLUS GALLUS (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsMoroz, Y.S. / Wu, Y. / van Nuland, N.A.J. / Korendovych, I.V.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: New Tricks for Old Proteins: Single Mutations in a Nonenzymatic Protein Give Rise to Various Enzymatic Activities.
Authors: Moroz, Y.S. / Dunston, T.T. / Makhlynets, O.V. / Moroz, O.V. / Wu, Y. / Yoon, J.H. / Olsen, A.B. / Mclaughlin, J.M. / Mack, K.L. / Gosavi, P.M. / Van Nuland, N.A.J. / Korendovych, I.V.
History
DepositionJul 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references / Other
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _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_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, C-TERMINAL DOMAIN, M144H MUTANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7043
Polymers8,6231
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein CALMODULIN, C-TERMINAL DOMAIN, M144H MUTANT /


Mass: 8623.391 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 76-144 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PEXP5-NT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: F2Z4K8, UniProt: P62149*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HBHA(CO)NH
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1713D (H)CCH-TOCSY
1813D N15-NOESY
1913D C13-NOESY
NMR detailsText: NONE

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Sample preparation

Details
Solution-IDContents
11.1 MM [U-100% 13C
2U-100% 15N] CCAMM144H, 95% H2O/5% D2O
Sample conditionsIonic strength: 100 mM / pH: 7.0 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, READ,RICE,SIMONSON,WARRENrefinement
CYANAstructure solution
NMRPipestructure solution
CNSstructure solution
X-PLORstructure solution
CARAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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