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- PDB-5to0: HTRA2 S276C mutant -

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Basic information

Entry
Database: PDB / ID: 5to0
TitleHTRA2 S276C mutant
ComponentsSerine protease HTRA2, mitochondrial
KeywordsHYDROLASE / Serine Protease / Parkinson Disease / Mitochondria / PDZ Dynamics
Function / homology
Function and homology information


HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of mitophagy in response to mitochondrial depolarization / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / regulation of autophagy of mitochondrion / CD40 receptor complex / ceramide metabolic process / : / programmed cell death / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand ...HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of mitophagy in response to mitochondrial depolarization / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / regulation of autophagy of mitochondrion / CD40 receptor complex / ceramide metabolic process / : / programmed cell death / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / serine-type endopeptidase complex / adult walking behavior / response to herbicide / execution phase of apoptosis / positive regulation of protein targeting to mitochondrion / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein autoprocessing / regulation of multicellular organism growth / negative regulation of cell cycle / neuron development / cellular response to interferon-beta / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / forebrain development / cellular response to retinoic acid / mitochondrion organization / serine-type peptidase activity / mitochondrial membrane / protein catabolic process / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / cellular response to growth factor stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / unfolded protein binding / cellular response to heat / cellular response to oxidative stress / peptidase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / cytoskeleton / positive regulation of apoptotic process / serine-type endopeptidase activity / chromatin / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / proteolysis / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease HTRA2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMerski, M. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)PortoNeuroDRIve@i3S Portugal
CitationJournal: Cell Death Dis / Year: 2017
Title: Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2.
Authors: Merski, M. / Moreira, C. / Abreu, R.M. / Ramos, M.J. / Fernandes, P.A. / Martins, L.M. / Pereira, P.J.B. / Macedo-Ribeiro, S.
History
DepositionOct 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Serine protease HTRA2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1892
Polymers35,9941
Non-polymers1951
Water1,35175
1
A: Serine protease HTRA2, mitochondrial
hetero molecules

A: Serine protease HTRA2, mitochondrial
hetero molecules

A: Serine protease HTRA2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5686
Polymers107,9823
Non-polymers5863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6370 Å2
ΔGint-18 kcal/mol
Surface area36760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.824, 83.824, 127.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Serine protease HTRA2, mitochondrial / High temperature requirement protein A2 / HtrA2 / Omi stress-regulated endoprotease / Serine ...High temperature requirement protein A2 / HtrA2 / Omi stress-regulated endoprotease / Serine protease 25 / Serine proteinase OMI


Mass: 35993.949 Da / Num. of mol.: 1 / Mutation: Mutation S276C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA2, OMI, PRSS25 / Production host: Escherichia coli (E. coli) / References: UniProt: O43464, HtrA2 peptidase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→63.1 Å / Num. obs: 26268 / % possible obs: 99.8 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 30
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3828

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCY

1lcy


Resolution: 1.9→47.894 Å / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 30.57
RfactorNum. reflection% reflection
Rfree0.1775 1333 5.07 %
Rwork0.1502 --
obs0.1576 26268 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 12 75 2238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012202
X-RAY DIFFRACTIONf_angle_d0.9213001
X-RAY DIFFRACTIONf_dihedral_angle_d14.3671336
X-RAY DIFFRACTIONf_chiral_restr0.061365
X-RAY DIFFRACTIONf_plane_restr0.005391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9009-1.96870.25491050.22982500X-RAY DIFFRACTION96
1.9687-2.04740.22641380.20732501X-RAY DIFFRACTION95
2.0474-2.14030.25151140.2112491X-RAY DIFFRACTION95
2.1403-2.25280.21141240.1962488X-RAY DIFFRACTION95
2.2528-2.39340.221460.19432520X-RAY DIFFRACTION94
2.3934-2.57740.20091570.18782442X-RAY DIFFRACTION94
2.5774-2.83530.1961500.18052450X-RAY DIFFRACTION94
2.8353-3.24210.18471400.16562495X-RAY DIFFRACTION95
3.2421-4.07150.16921370.13232483X-RAY DIFFRACTION95
4.0715-15.17250.15551210.11172495X-RAY DIFFRACTION95

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