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Yorodumi- PDB-6z0x: HtrA1 inactive protease domain S328A with CARASIL mutations D174R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z0x | ||||||
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Title | HtrA1 inactive protease domain S328A with CARASIL mutations D174R R274Q | ||||||
Components | Serine protease HTRA1 | ||||||
Keywords | HYDROLASE / 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 / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development ...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 / molecular function activator activity / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Vetter, I.R. / Stege, P. / Ingendahl, L. / Ehrmann, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z0x.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z0x.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 6z0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z0x_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 6z0x_full_validation.pdf.gz | 468.1 KB | Display | |
Data in XML | 6z0x_validation.xml.gz | 22 KB | Display | |
Data in CIF | 6z0x_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/6z0x ftp://data.pdbj.org/pub/pdb/validation_reports/z0/6z0x | HTTPS FTP |
-Related structure data
Related structure data | 6z0eC 6z0yC 3tjoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.6 M ammonium sulfate, 100 mM Citrate pH 4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91504 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91504 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 233.06 Å2 / Biso mean: 132.071 Å2 / Biso min: 82.53 Å2
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Refinement step | Cycle: final / Resolution: 3.1→48.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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