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- PDB-1x37: Structure of Bacillus subtilis Lon protease SSD domain -

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Basic information

Entry
Database: PDB / ID: 1x37
TitleStructure of Bacillus subtilis Lon protease SSD domain
ComponentsATP-dependent protease La 1
KeywordsHYDROLASE / AAA+ superfamily / protease / SSD domain / solution structure
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Lon protease, bacterial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. ...Lon protease, bacterial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Helicase, Ruva Protein; domain 3 - #60 / PUA-like superfamily / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsWang, I. / Lou, Y.C. / Lo, S.C. / Lee, Y.L. / Wu, S.H. / Chen, C.
CitationJournal: to be published
Title: Structural basis and DNA binding property of SSD domain of Bacillus subtilis Lon protease
Authors: Wang, I. / Lou, Y.C. / Lo, S.C. / Lee, Y.L. / Wu, S.H. / Chen, C.
History
DepositionApr 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: ATP-dependent protease La 1


Theoretical massNumber of molelcules
Total (without water)14,3961
Polymers14,3961
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)16 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein ATP-dependent protease La 1 / Lon protease


Mass: 14395.650 Da / Num. of mol.: 1 / Fragment: SSD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET-21a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37945, endopeptidase La

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1313D 15N-separated NOESY
1423D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM BsLonSSD U-15N, 13C; 50mM phosphate buffer with 100mM NaCl, 50mM Arg/Glu, 5mM DTT90% H2O/10% D2O
21.5mM BsLonSSD U-15N, 13C; 50mM phosphate buffer with 100mM NaCl, 50mM Arg/Glu, 5mM DTT100% D2O
Sample conditionspH: 5.8 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
XwinNMR3.5Brukerprocessing
AURELIA3.1.6Brukerdata analysis
NMRPipeDelaglio, F.processing
NMRView5.2.2Johnson, B. A.data analysis
X-PLOR3.851Brunger, A. T.structure solution
X-PLOR3.851Brunger, A. T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1157 restraints, 968 are NOE-derived distance constraints, 121 dihedral angle restraints,68 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 16

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