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- PDB-6z0x: HtrA1 inactive protease domain S328A with CARASIL mutations D174R... -

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Basic information

Entry
Database: PDB / ID: 6z0x
TitleHtrA1 inactive protease domain S328A with CARASIL mutations D174R R274Q
ComponentsSerine protease HTRA1
KeywordsHYDROLASE / Hydrolase Protease HtrA family CARASIL mutations trimerization
Function / homology
Function and homology information


chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / placenta development / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway ...chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / placenta development / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / collagen-containing extracellular matrix / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C / Kazal domain superfamily ...Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / PDZ domain 6 / Kazal type serine protease inhibitors / PDZ domain / Peptidase S1C / Kazal domain superfamily / Trypsin-like peptidase domain / Kazal domain / Kazal domain profile. / Growth factor receptor cysteine-rich domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Serine protease HTRA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVetter, I.R. / Stege, P. / Ingendahl, L. / Ehrmann, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1093 Germany
CitationJournal: To Be Published
Title: Repair strategies addressing pathogenic protein conformations
Authors: Ingendahl, L. / Beaufort, N. / Kuszner, M. / Vetter, I.R. / Stege, P. / Ruiz-Blanco, Y.B. / Bravo-Rodriguez, K. / Beuck, C. / Schillinger, J. / Rey, J. / Roberti, A. / Hagemeier, B. / Hu, X.- ...Authors: Ingendahl, L. / Beaufort, N. / Kuszner, M. / Vetter, I.R. / Stege, P. / Ruiz-Blanco, Y.B. / Bravo-Rodriguez, K. / Beuck, C. / Schillinger, J. / Rey, J. / Roberti, A. / Hagemeier, B. / Hu, X.-Y. / Clausen, T. / Sanchez-Garcia, E. / Schmuck, C. / Dichgans, M. / Ehrmann, M.
History
DepositionMay 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 HTRA1
B: Serine protease HTRA1
C: Serine protease HTRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,84312
Polymers76,9783
Non-polymers8659
Water25214
1
A: Serine protease HTRA1
hetero molecules

A: Serine protease HTRA1
hetero molecules

A: Serine protease HTRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,41918
Polymers76,9783
Non-polymers1,44115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area8420 Å2
ΔGint-255 kcal/mol
Surface area28810 Å2
MethodPISA
2
B: Serine protease HTRA1
hetero molecules

B: Serine protease HTRA1
hetero molecules

B: Serine protease HTRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,84312
Polymers76,9783
Non-polymers8659
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 area7830 Å2
ΔGint-187 kcal/mol
Surface area26520 Å2
MethodPISA
3
C: Serine protease HTRA1
hetero molecules

C: Serine protease HTRA1
hetero molecules

C: Serine protease HTRA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2666
Polymers76,9783
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area7070 Å2
ΔGint-81 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.520, 103.520, 147.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-401-

SO4

21A-507-

HOH

31B-503-

HOH

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Components

#1: Protein Serine protease HTRA1 / High-temperature requirement A serine peptidase 1 / L56 / Serine protease 11


Mass: 25659.359 Da / Num. of mol.: 3 / Mutation: D174R R274Q S328A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.6 M ammonium sulfate, 100 mM Citrate pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91504 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91504 Å / Relative weight: 1
ReflectionResolution: 3.1→48.88 Å / Num. obs: 15480 / % possible obs: 95.4 % / Redundancy: 20.537 % / Biso Wilson estimate: 110.027 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.117 / Χ2: 1.012 / Net I/σ(I): 17.4 / Num. measured all: 317918
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.1921.9941.8071.521073311994880.7281.8540.7
3.19-3.2721.381.7251.625121117511750.7741.766100
3.27-3.3721.1231.2652.3223763112511250.841.296100
3.37-3.4720.4410.9653.2122219108710870.9110.989100
3.47-3.5819.7210.7844.0121338108210820.9460.804100
3.58-3.7120.960.764.6621086101710060.9550.77998.9
3.71-3.8521.4040.5116.4121575100810080.9770.523100
3.85-4.0120.3580.3719.15191579509410.9880.38199.1
4.01-4.1920.4230.21814.42187899209200.9940.224100
4.19-4.3918.9470.15319.27166548808790.9970.15799.9
4.39-4.6320.4760.11924.73170778348340.9980.122100
4.63-4.9120.8470.10728.23166577997990.9980.11100
4.91-5.2520.8120.09829.56152767347340.9980.1100
5.25-5.6719.9890.09729.06142127117110.9980.1100
5.67-6.2120.3720.08932.02129366356350.9990.091100
6.21-6.9421.3320.07140.32123945815810.9990.072100
6.94-8.0220.4290.05944.121052151551510.061100
8.02-9.8219.0670.04753.52825643343310.048100
9.82-13.8819.9650.03959.73676833933910.041100
13.88-48.8818.0110.04358.3233861941880.9990.04496.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TJO

3tjo


Resolution: 3.1→48.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.897 / SU B: 25.343 / SU ML: 0.415 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.475
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 814 5 %RANDOM
Rwork0.2237 ---
obs0.2261 15452 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 233.06 Å2 / Biso mean: 132.071 Å2 / Biso min: 82.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å21.09 Å20 Å2
2--2.18 Å2-0 Å2
3----7.07 Å2
Refinement stepCycle: final / Resolution: 3.1→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 45 14 4661
Biso mean--165.08 113.78 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0134721
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174577
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.6346396
X-RAY DIFFRACTIONr_angle_other_deg1.0021.5810626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0425596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.47923.223211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12315839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.21522
X-RAY DIFFRACTIONr_chiral_restr0.030.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02885
X-RAY DIFFRACTIONr_mcbond_it2.7214.0112396
X-RAY DIFFRACTIONr_mcbond_other2.7214.0092395
X-RAY DIFFRACTIONr_mcangle_it4.85421.0012985
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 60 -
Rwork0.363 1129 -
all-1189 -
obs--100 %

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