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- PDB-5m3o: HTRA2 A141S mutant structure -

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Basic information

Entry
Database: PDB / ID: 5m3o
TitleHTRA2 A141S mutant structure
ComponentsSerine protease HTRA2, mitochondrial
KeywordsHYDROLASE / Serine Protease Parkinson Disease Mitochondria PDZ domain Dynamics
Function / homology
Function and homology information


HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of type 2 mitophagy / ceramide metabolic process / regulation of autophagy of mitochondrion / CD40 receptor complex / mitochondrial protein catabolic process / programmed cell death / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / serine-type endopeptidase complex ...HtrA2 peptidase / pentacyclic triterpenoid metabolic process / negative regulation of type 2 mitophagy / ceramide metabolic process / regulation of autophagy of mitochondrion / CD40 receptor complex / mitochondrial protein catabolic 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 / positive regulation of protein targeting to mitochondrion / execution phase of apoptosis / forebrain development / negative regulation of cell cycle / protein autoprocessing / ubiquitin ligase inhibitor activity / protein serine/threonine kinase inhibitor activity / regulation of multicellular organism growth / positive regulation of execution phase of apoptosis / Mitochondrial unfolded protein response (UPRmt) / neuron development / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to interferon-beta / cellular response to retinoic acid / serine-type peptidase activity / Mitochondrial protein degradation / mitochondrion organization / protein catabolic process / cellular response to growth factor stimulus / mitochondrial membrane / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage / unfolded protein binding / peptidase activity / cellular response to heat / cellular response to oxidative stress / neuron apoptotic process / negative regulation of neuron apoptotic process / cytoskeleton / intracellular signal transduction / positive regulation of apoptotic process / serine-type endopeptidase activity / endoplasmic reticulum membrane / chromatin / endoplasmic reticulum / mitochondrion / proteolysis / identical protein binding / nucleus / membrane / 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: 1.7 Å
AuthorsMerski, M. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
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 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 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)36,4562
Polymers36,2611
Non-polymers1951
Water2,126118
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)109,3696
Polymers108,7833
Non-polymers5863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area6220 Å2
ΔGint-22 kcal/mol
Surface area36160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.291, 84.291, 127.978
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: 36261.145 Da / Num. of mol.: 1 / Mutation: Mutation A141S
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


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


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
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: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→63.4 Å / Num. obs: 37293 / % possible obs: 100 % / Redundancy: 5.4 % / Net I/σ(I): 17.5

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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: 1.7→31.704 Å / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 28.57
RfactorNum. reflection% reflection
Rfree0.2003 1883 5.05 %
Rwork0.1683 --
obs0.1704 37292 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→31.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 12 118 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112222
X-RAY DIFFRACTIONf_angle_d1.0753039
X-RAY DIFFRACTIONf_dihedral_angle_d14.2361355
X-RAY DIFFRACTIONf_chiral_restr0.061372
X-RAY DIFFRACTIONf_plane_restr0.007395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.7460.31721310.312737X-RAY DIFFRACTION95
1.746-1.79730.28851540.26532724X-RAY DIFFRACTION95
1.7973-1.85530.23191200.23922731X-RAY DIFFRACTION96
1.8553-1.92150.25711370.22442731X-RAY DIFFRACTION95
1.9215-1.99830.23861630.21292695X-RAY DIFFRACTION94
1.9983-2.08910.21081460.20842746X-RAY DIFFRACTION95
2.0891-2.1990.23551430.20732692X-RAY DIFFRACTION95
2.199-2.33640.20051600.20382728X-RAY DIFFRACTION94
2.3364-2.51630.23721540.19042712X-RAY DIFFRACTION95
2.5163-2.76840.18591510.19692685X-RAY DIFFRACTION95
2.7684-3.16660.20391450.17332742X-RAY DIFFRACTION95
3.1666-3.98050.17731430.13322719X-RAY DIFFRACTION95
3.9805-16.60610.1661360.10982734X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.90581.32852.27631.39680.24121.6328-0.1696-0.00560.19520.05610.0335-0.1309-0.07580.03620.06070.10040.03080.01640.11710.00570.155116.4054-44.9934-15.5988
25.02951.5575.16580.48191.65.30420.4883-0.5713-0.2010.0393-0.12270.06020.7224-0.6679-0.32240.1772-0.0117-0.02820.2267-0.03740.243627.5263-36.83351.2756
33.00510.91661.12571.42090.34061.489-0.1187-0.06110.28770.11050.0085-0.2431-0.09560.29260.08160.1658-0.0133-0.05860.2018-0.0090.242919.0648-33.2016-10.7208
43.43831.6634-1.53172.77131.79635.61710.195-0.2180.37880.1396-0.12220.0879-0.2265-0.14410.00260.14010.0101-0.03730.124-0.03750.20925.0625-34.5305-9.4823
50.78430.19931.02941.31161.43664.341-0.1611-0.32330.64120.1473-0.19870.3218-0.2638-0.25860.27510.23370.036-0.13980.2625-0.14320.54696.5626-26.8554-1.4339
65.57480.37133.21432.61360.65464.16510.2717-0.3162-0.0339-0.1464-0.4510.81380.0491-0.50060.18140.34660.0245-0.15350.3733-0.18640.552910.8121-21.289611.3526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 140 through 170 )
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 188 )
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 274 )
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 329 )
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 396 )
6X-RAY DIFFRACTION6chain 'A' and (resid 397 through 459 )

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