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Yorodumi- PDB-3num: Substrate induced remodeling of the active site regulates HtrA1 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3num | ||||||
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Title | Substrate induced remodeling of the active site regulates HtrA1 activity | ||||||
Components | Serine protease HTRA1 | ||||||
Keywords | HYDROLASE / serine protease / DegP / HtrA / protease | ||||||
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: 2.75 Å | ||||||
Authors | Truebestein, L. / Tennstaedt, A. / Hauske, P. / Krojer, T. / Kaiser, M. / Clausen, T. / Ehrmann, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Substrate-induced remodeling of the active site regulates human HTRA1 activity. Authors: Truebestein, L. / Tennstaedt, A. / Monig, T. / Krojer, T. / Canellas, F. / Kaiser, M. / Clausen, T. / Ehrmann, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3num.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3num.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 3num.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3num_validation.pdf.gz | 424.6 KB | Display | wwPDB validaton report |
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Full document | 3num_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | 3num_validation.xml.gz | 9 KB | Display | |
Data in CIF | 3num_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/3num ftp://data.pdbj.org/pub/pdb/validation_reports/nu/3num | HTTPS FTP |
-Related structure data
Related structure data | 3nwuC 3nziC 1lcyS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36425.629 Da / Num. of mol.: 1 / Fragment: protease and pdz domain (unp residue 158-480) / Mutation: S328A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.89 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.0M LiSO4, 0.1M sodium citrate pH5.6, 0.5M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 12716 / Num. obs: 12716 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.6 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LCY Resolution: 2.75→19.32 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 22.494 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→19.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.746→2.816 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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