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- PDB-6z0e: HtrA1 inactive protease domain S328A with CARASIL mutation R274Q -

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Basic information

Entry
Database: PDB / ID: 6z0e
TitleHtrA1 inactive protease domain S328A with CARASIL mutation 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: 2.6 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 8, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3154
Polymers51,2352
Non-polymers802
Water59433
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)76,9726
Polymers76,8523
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5400 Å2
ΔGint-41 kcal/mol
Surface area25700 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)76,9726
Polymers76,8523
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5650 Å2
ΔGint-37 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.860, 109.860, 114.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-401-

CA

21B-401-

CA

31A-520-

HOH

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Components

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


Mass: 25617.252 Da / Num. of mol.: 2 / Mutation: 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1 M LiCl, 20% PEG6000, 0.1M Citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.02 Å / Num. obs: 15840 / % possible obs: 100 % / Redundancy: 10.35 % / Biso Wilson estimate: 47.529 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.329 / Rrim(I) all: 0.346 / Χ2: 0.981 / Net I/σ(I): 9.44 / Num. measured all: 163941 / Scaling rejects: 144
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
2.6-2.6710.2722.534112059117411740.372.667100
2.67-2.749.9561.8531.3811549116011600.4821.955100
2.74-2.829.3691.6841.5110353110511050.5831.782100
2.82-2.9110.3371.3881.9110999106410640.6361.46100
2.91-310.751.1632.4711288105010500.7521.222100
3-3.1110.710.913.3110721100110010.8720.956100
3.11-3.2310.6260.7833.9810669100410040.8680.822100
3.23-3.3610.5250.595.4597999319310.9410.62100
3.36-3.5110.3780.4427.5292168888880.9670.464100
3.51-3.689.4880.3778.1583688828820.9670.399100
3.68-3.8810.5270.31110.0385168098090.9810.327100
3.88-4.1110.9940.23213.4884767717710.990.243100
4.11-4.3910.8180.15519.3878867297290.9950.162100
4.39-4.7510.6530.12122.2870956666660.9970.127100
4.75-5.29.9920.12621.0562556266260.9960.133100
5.2-5.819.8270.1518.3355825685680.9940.159100
5.81-6.7111.0360.14120.2554964984980.9960.148100
6.71-8.2210.7140.10724.4545004214200.9970.11299.8
8.22-11.639.6660.05342.4830353143140.9990.056100
11.63-49.0211.550.04752.220791821800.9990.04998.9

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3794refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TJO

3tjo


Resolution: 2.6→49.02 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 30.36
RfactorNum. reflection% reflection
Rfree0.2647 787 4.97 %
Rwork0.2378 --
obs0.2391 15824 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.25 Å2 / Biso mean: 59.7704 Å2 / Biso min: 25.53 Å2
Refinement stepCycle: final / Resolution: 2.6→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 2 33 2961
Biso mean--45.4 41.51 -
Num. residues----384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.760.43211310.377725202651
2.76-2.980.38871320.335924932625
2.98-3.280.32291280.285324792607
3.28-3.750.27481330.247525182651
3.75-4.720.21341330.201825282661
4.73-49.020.2151300.192624992629

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