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- PDB-1qzm: alpha-domain of ATPase -

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Basic information

Entry
Database: PDB / ID: 1qzm
Titlealpha-domain of ATPase
ComponentsATP-dependent protease LaEndopeptidase La
KeywordsHYDROLASE / oligomerization domain / AAA+ protein / ATP-dependent protease
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) / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å
AuthorsBotos, I. / Melnikov, E.E. / Cherry, S. / Khalatova, A.G. / Rasulova, F.S. / Tropea, J.E. / Maurizi, M.R. / Rotanova, T.V. / Gustchina, A. / Wlodawer, A.
CitationJournal: J.Struct.Biol.
Title: Crystal structure of the AAA+ alpha domain of E. coli Lon protease at 1.9A resolution.
Authors: Botos, I. / Melnikov, E.E. / Cherry, S. / Khalatova, A.G. / Rasulova, F.S. / Tropea, J.E. / Maurizi, M.R. / Rotanova, T.V. / Gustchina, A. / Wlodawer, A.
History
DepositionSep 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ATP-dependent protease La


Theoretical massNumber of molelcules
Total (without water)10,8391
Polymers10,8391
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.430, 46.430, 85.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 10838.533 Da / Num. of mol.: 1 / Fragment: alpha domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LON / Plasmid: pBR-lonS679A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A9M0, endopeptidase La
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 3000, CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2003 / Details: MSC/Osmic mirror
RadiationMonochromator: MSC/Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 7808 / Num. obs: 6595 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→2.02 Å / % possible all: 89.2

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
SHELXLrefinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→10 Å / Num. parameters: 3423 / Num. restraintsaints: 3088 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 787 11.9 %RANDOM
Rwork0.179 ---
obs0.184 6595 84.8 %-
all-7808 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 852
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 0 0 90 852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.038
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0238
X-RAY DIFFRACTIONs_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.096
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.9→2.02 Å

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