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- PDB-2x36: Structure of the proteolytic domain of the Human Mitochondrial Lo... -

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Basic information

Entry
Database: PDB / ID: 2x36
TitleStructure of the proteolytic domain of the Human Mitochondrial Lon protease
ComponentsLON PROTEASE HOMOLOG, MITOCHONDRIAL
KeywordsHYDROLASE / CATALYTIC DYAD / TRANSIT PEPTIDE / MITOCHONDRIA
Function / homology
Function and homology information


oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / response to aluminum ion / endopeptidase La / G-quadruplex DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins ...oxidation-dependent protein catabolic process / PH domain binding / mitochondrial protein catabolic process / response to aluminum ion / endopeptidase La / G-quadruplex DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / mitochondrial nucleoid / insulin receptor substrate binding / Mitochondrial unfolded protein response (UPRmt) / chaperone-mediated protein complex assembly / DNA polymerase binding / response to hormone / Mitochondrial protein degradation / negative regulation of insulin receptor signaling pathway / proteolysis involved in protein catabolic process / mitochondrion organization / protein catabolic process / ADP binding / single-stranded DNA binding / cellular response to oxidative stress / sequence-specific DNA binding / response to hypoxia / single-stranded RNA binding / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Lon protease homologue, chloroplastic/mitochondrial / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / 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 homologue, chloroplastic/mitochondrial / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / 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 N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Ribosomal Protein S5; domain 2 - #10 / PUA-like superfamily / Ribosomal Protein S5; domain 2 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lon protease homolog, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarcia, J. / Ondrovicova, G. / Blagova, E. / Levdikov, V.M. / Bauer, J.A. / Kutejova, E. / Wilkinson, A.J. / Wilson, K.S.
CitationJournal: Protein Sci. / Year: 2010
Title: Structure of the Catalytic Domain of the Human Mitochondrial Lon Protease: Proposed Relation of Oligomer Formation and Activity.
Authors: Garcia-Nafria, J. / Ondrovicova, G. / Blagova, E. / Levdikov, V.M. / Bauer, J.A. / Suzuki, C.K. / Kutejova, E. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionJan 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LON PROTEASE HOMOLOG, MITOCHONDRIAL
B: LON PROTEASE HOMOLOG, MITOCHONDRIAL
C: LON PROTEASE HOMOLOG, MITOCHONDRIAL
D: LON PROTEASE HOMOLOG, MITOCHONDRIAL
E: LON PROTEASE HOMOLOG, MITOCHONDRIAL
F: LON PROTEASE HOMOLOG, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)134,5546
Polymers134,5546
Non-polymers00
Water5,909328
1
A: LON PROTEASE HOMOLOG, MITOCHONDRIAL
B: LON PROTEASE HOMOLOG, MITOCHONDRIAL
E: LON PROTEASE HOMOLOG, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)67,2773
Polymers67,2773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-15.9 kcal/mol
Surface area23770 Å2
MethodPISA
2
C: LON PROTEASE HOMOLOG, MITOCHONDRIAL
D: LON PROTEASE HOMOLOG, MITOCHONDRIAL
F: LON PROTEASE HOMOLOG, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)67,2773
Polymers67,2773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-16.6 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.800, 83.750, 105.490
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
LON PROTEASE HOMOLOG, MITOCHONDRIAL / LON PROTEASE-LIKE PROTEIN / LONP / LONHS / SERINE PROTEASE 15 / MITOCHONDRIAL ATP-DEPENDENT PROTEASE LON


Mass: 22425.717 Da / Num. of mol.: 6 / Fragment: PROTEOLYTIC DOMAIN, RESIDUES 753-959
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA II
References: UniProt: P36776, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.53 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M BIS-TRIS PROPANOL PH 6.5, 0.25 M SODIUM ACETATE, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395, 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.321
11-h,-k,l20.679
ReflectionResolution: 2→2.11 Å / Num. obs: 82419 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RRE

1rre


Resolution: 2→34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.377 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 4394 5.4 %RANDOM
Rwork0.19355 ---
obs0.19549 77152 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.803 Å2
Baniso -1Baniso -2Baniso -3
1-16.64 Å20 Å21.51 Å2
2--17.57 Å20 Å2
3----34.21 Å2
Refinement stepCycle: LAST / Resolution: 2→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8297 0 0 328 8625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0228558
X-RAY DIFFRACTIONr_bond_other_d0.0010.025702
X-RAY DIFFRACTIONr_angle_refined_deg2.0951.96811625
X-RAY DIFFRACTIONr_angle_other_deg1.196313966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81551104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86223.394327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.004151401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5681548
X-RAY DIFFRACTIONr_chiral_restr0.1390.21352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4745492
X-RAY DIFFRACTIONr_mcbond_other1.58642250
X-RAY DIFFRACTIONr_mcangle_it5.68668847
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.91183066
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.057102777
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 371 -
Rwork0.23 5400 -
obs--95.18 %

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