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- PDB-2mk6: Structure determination of substrate binding domain of MecA -

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Basic information

Entry
Database: PDB / ID: 2mk6
TitleStructure determination of substrate binding domain of MecA
ComponentsAdapter protein MecA
KeywordsGENE REGULATION / MecA / competence / proteolysis
Function / homologyNegative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / Adapter protein MecA / :
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsZhang, Y.-H. / Zhang, Y. / Jin, C. / Shi, Y.
CitationJournal: To be Published
Title: NMR structure and interaction analysis of the substrate binding domain of MecA
Authors: Zhang, Y.-H. / Zhang, Y. / Jin, C. / Shi, Y.
History
DepositionJan 29, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Adapter protein MecA


Theoretical massNumber of molelcules
Total (without water)10,9041
Polymers10,9041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Adapter protein MecA


Mass: 10904.178 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-83)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: spizizenii ATCC 6633 / Gene: BSU6633_15767, mecA / Plasmid: pYN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5N397, UniProt: A0A0J9X1W8*PLUS

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11313D (H)CCH-COSY
11413D HN(COCA)CB

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Sample preparation

DetailsContents: 1.0 mM [U-13C; U-15N] MecA-NTD, 140 mM sodium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMMecA-NTD-1[U-13C; U-15N]1
140 mMsodium chloride-21
10 mMsodium phosphate-31
1.8 mMpotassium phosphate-41
Sample conditionsIonic strength: 0.3 / pH: 7.3 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
CCPN_Analysis2CCPNchemical shift assignment
CCPN_Analysis2CCPNdata analysis
CCPN_Analysis2CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MARSMarkus Zweckstetterchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichgeometry optimization
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 3573 / NOE intraresidue total count: 1507 / NOE long range total count: 727 / NOE medium range total count: 525 / NOE sequential total count: 814 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 75
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.33 Å

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