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- PDB-2m3s: Calmodulin, i85l, f92e, h107i, l112r, a128t, m144r mutant -

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Basic information

Entry
Database: PDB / ID: 2m3s
TitleCalmodulin, i85l, f92e, h107i, l112r, a128t, m144r mutant
ComponentsCalmodulin
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, matrix relaxation
Model detailslowest energy, model1
AuthorsMoroz, Y.S. / Wu, Y. / Cheng, H. / Roder, H. / Korendovych, I.V.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: A single mutation in a regulatory protein produces evolvable allosterically regulated catalyst of nonnatural reaction.
Authors: Moroz, O.V. / Moroz, Y.S. / Wu, Y. / Olsen, A.B. / Cheng, H. / Mack, K.L. / McLaughlin, J.M. / Raymond, E.A. / Zhezherya, K. / Roder, H. / Korendovych, I.V.
History
DepositionJan 25, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2705
Polymers17,1101
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin / / CaM


Mass: 17109.791 Da / Num. of mol.: 1 / Fragment: UNP residues 1-149 / Mutation: I85L, F92E, H107I, L107I, A128T, M144R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALM, CAM, RCJMB04_24e7 / Plasmid: pEXP5-NT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62149
#2: 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D HNCO
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D N15/C13-NOESY
11022D 1H-15N HSQC IPAP
11123D CCH TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.68 mM [U-100% 13C; U-100% 15N] protein_1, 0.005 % DSS, 20 mM HEPES, 100 mM sodium chloride, 10 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 15N] protein_1, 0.005 % DSS, 20 mM HEPES, 100 mM sodium chloride, 10 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.68 mMentity_1-1[U-100% 13C; U-100% 15N]1
0.005 %DSS-21
20 mMHEPES-31
100 mMsodium chloride-41
10 mMcalcium cloride-51
0.5 mMentity_1-6[U-100% 15N]2
0.005 %DSS-72
20 mMHEPES-82
100 mMsodium chloride-92
10 mMcalcium cloride-102
Sample conditionsIonic strength: 0.1 / pH: 6.91 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOLKoradi, Billeter and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichprocessing
PSVSBhattacharya and Montelionedata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, matrix relaxation / Software ordinal: 1
NMR constraintsNOE constraints total: 2202 / NOE intraresidue total count: 551 / NOE long range total count: 485 / NOE medium range total count: 563 / NOE sequential total count: 603 / Protein phi angle constraints total count: 135 / Protein psi angle constraints total count: 135
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 40 / Conformers submitted total number: 20

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