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- PDB-2m98: NMR Structure of BeF3 Activated Sma0114 -

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Basic information

Entry
Database: PDB / ID: 2m98
TitleNMR Structure of BeF3 Activated Sma0114
ComponentsTwo-component response regulator
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Two-component response regulator
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsSheftic, S.R. / Gage, D.J. / Alexandrescu, A.T.
CitationJournal: Biochemistry / Year: 2014
Title: NMR Structure of the HWE Kinase Associated Response Regulator Sma0114 in Its Activated State.
Authors: Sheftic, S.R. / White, E. / Gage, D.J. / Alexandrescu, A.T.
History
DepositionJun 4, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
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_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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7133
Polymers13,6071
Non-polymers1062
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Two-component response regulator


Mass: 13606.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RA0058, SMa0114 / Production host: Escherichia coli (E. coli) / References: UniProt: Q930Y6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

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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-1H NOESY
1323D HN(CA)CB
1423D 1H-15N NOESY
1512D 1H-1H NOESY
1623D 1H-13C NOESY
1712D DQF-COSY
1812D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM CALCIUM ION, 36 mM BERYLLIUM TRIFLUORIDE ION, 0.5 mM [U-100% 15N] protein, 1 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM CALCIUM ION, 36 mM BERYLLIUM TRIFLUORIDE ION, 0.5 mM [U-100% 13C; U-100% 15N] protein, 1 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMCALCIUM ION-11
36 mMBERYLLIUM TRIFLUORIDE ION-21
0.5 mMentity_1-3[U-100% 15N]1
1 mMDTT-41
0.02 %sodium azide-51
1.5 mMCALCIUM ION-62
36 mMBERYLLIUM TRIFLUORIDE ION-72
0.5 mMentity_1-8[U-100% 13C; U-100% 15N]2
1 mMDTT-92
0.02 %sodium azide-102
Sample conditionsIonic strength: 38 / pH: 6 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 26

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