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- PDB-6n2i: Lon protease AAA+ domain -

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Basic information

Entry
Database: PDB / ID: 6n2i
TitleLon protease AAA+ domain
ComponentsDNA-binding ATP-dependent protease La
KeywordsHYDROLASE / Lon protease / AAA+ domain
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity ...endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / DNA binding / ATP binding / cytosol / 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) / PUA-like superfamily / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Lon protease / Lon protease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBotos, I. / Li, M. / Wlodawer, A. / Gustchina, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: Febs Open Bio / Year: 2019
Title: New insights into structural and functional relationships between LonA proteases and ClpB chaperones.
Authors: Rotanova, T.V. / Andrianova, A.G. / Kudzhaev, A.M. / Li, M. / Botos, I. / Wlodawer, A. / Gustchina, A.
History
DepositionNov 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding ATP-dependent protease La
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2302
Polymers38,8031
Non-polymers4271
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-5 kcal/mol
Surface area17530 Å2
Unit cell
Length a, b, c (Å)88.600, 88.600, 67.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DNA-binding ATP-dependent protease La


Mass: 38802.988 Da / Num. of mol.: 1 / Fragment: UNP Residues 62-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lon_1, NCTC9775_02029 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A376KCZ4, UniProt: P0A9M0*PLUS, endopeptidase La
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.82 % / Description: rod
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) PEG 400, 0.2 M Lithium sulfate, 0.1 M sodium Cacodylate

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 3.5→44.3 Å / Num. obs: 3856 / % possible obs: 100 % / Redundancy: 11.1 % / Net I/σ(I): 19
Reflection shellResolution: 3.5→4.4 Å

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.10.2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPL

4ypl


Resolution: 3.5→44.3 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.93
Details: While the interactions are not very precise at atomic level, the structure still provides valuable information about the quaternary state of the molecule.
RfactorNum. reflection% reflection
Rfree0.3254 219 5.68 %
Rwork0.2845 --
obs0.2866 3856 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2669 0 27 0 2696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032736
X-RAY DIFFRACTIONf_angle_d0.6613683
X-RAY DIFFRACTIONf_dihedral_angle_d13.7041716
X-RAY DIFFRACTIONf_chiral_restr0.041412
X-RAY DIFFRACTIONf_plane_restr0.004471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-4.40930.38931190.33881776X-RAY DIFFRACTION98
4.4093-44.30350.28441000.25551861X-RAY DIFFRACTION100

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