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- PDB-5fht: HtrA2 protease mutant V226K -

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Basic information

Entry
Database: PDB / ID: 5fht
TitleHtrA2 protease mutant V226K
ComponentsSerine protease HTRA2, mitochondrial
KeywordsHYDROLASE / APOPTOSIS
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 / ceramide metabolic process / CD40 receptor complex / : / 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 / ceramide metabolic process / CD40 receptor complex / : / 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 / 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 / serine-type peptidase activity / mitochondrion organization / 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 oxidative stress / cellular response to heat / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGolik, P. / Dubin, G. / Zurawa-Janicka, D. / Lipinska, B. / Jarzab, M. / Wenta, T. / Gieldon, A. / Ciarkowski, A.
CitationJournal: Plos One / Year: 2016
Title: Distinct 3D Architecture and Dynamics of the Human HtrA2(Omi) Protease and Its Mutated Variants.
Authors: Gieldon, A. / Zurawa-Janicka, D. / Jarzab, M. / Wenta, T. / Golik, P. / Dubin, G. / Lipinska, B. / Ciarkowski, J.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease HTRA2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5275
Polymers36,2341
Non-polymers2934
Water3,603200
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-19 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.010, 86.010, 126.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-697-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 36234.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA2, OMI, PRSS25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43464, HtrA2 peptidase

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Non-polymers , 5 types, 204 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MES, NaCl, KH2PO4, NaH2PO4 / PH range: 6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→14.57 Å / Num. obs: 25396 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 7.4
Reflection shellHighest resolution: 1.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-alanine model of 1LCY

1lcy


Resolution: 1.95→14.57 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.865 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22753 1297 5.1 %RANDOM
Rwork0.17488 ---
obs0.17743 24098 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.372 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→14.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 15 200 2459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192343
X-RAY DIFFRACTIONr_bond_other_d0.0010.022305
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9783211
X-RAY DIFFRACTIONr_angle_other_deg0.94135279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44723.40494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74315372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3021520
X-RAY DIFFRACTIONr_chiral_restr0.2510.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
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_it2.6572.6771215
X-RAY DIFFRACTIONr_mcbond_other2.6562.6761214
X-RAY DIFFRACTIONr_mcangle_it3.5913.9881518
X-RAY DIFFRACTIONr_mcangle_other3.593.9891519
X-RAY DIFFRACTIONr_scbond_it3.6483.0931128
X-RAY DIFFRACTIONr_scbond_other3.6483.0931128
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2954.4821685
X-RAY DIFFRACTIONr_long_range_B_refined7.24322.4352554
X-RAY DIFFRACTIONr_long_range_B_other7.10621.9132482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 89 -
Rwork0.184 1793 -
obs--99.47 %
Refinement TLS params.Method: refined / Origin x: 8.6638 Å / Origin y: 19.9934 Å / Origin z: 45.4654 Å
111213212223313233
T0.0542 Å2-0.0054 Å2-0.0107 Å2-0.0103 Å20.0104 Å2--0.0186 Å2
L0.1012 °20.0427 °2-0.1306 °2-0.555 °2-0.3785 °2--0.569 °2
S0.0031 Å °0.0082 Å °0.0256 Å °-0.0657 Å °-0.036 Å °-0.0302 Å °-0.0315 Å °0.0303 Å °0.033 Å °

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