+Open data
-Basic information
Entry | Database: PDB / ID: 7xs2 | ||||||
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Title | Monomer structure of HtrA from Helicobacter pylori | ||||||
Components | Periplasmic serine endoprotease DegP-like | ||||||
Keywords | HYDROLASE / serine protease | ||||||
Function / homology | Function and homology information peptidase Do / periplasmic space / serine-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Cui, L. / Liu, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 Title: Crystal structures and solution conformations of HtrA from Helicobacter pylori reveal pH-dependent oligomeric conversion and conformational rearrangements. Authors: Cui, L. / Shi, X. / Li, H. / Wang, S. / Guo, L. / Lan, Z. / Dai, Y. / Zhang, Q. / Wu, Y. / Liu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xs2.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xs2.ent.gz | 128.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/7xs2 ftp://data.pdbj.org/pub/pdb/validation_reports/xs/7xs2 | HTTPS FTP |
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-Related structure data
Related structure data | 7xs0C 3pv2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47854.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: HP_1019 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25663, peptidase Do |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.4 Details: 0.1 M sodium citrate, pH 3.4, 2.7 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→75.59 Å / Num. obs: 32753 / % possible obs: 100 % / Redundancy: 35.7 % / CC1/2: 0.999 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.15→2.27 Å / Num. unique obs: 4671 / Rpim(I) all: 0.421 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PV2 Resolution: 2.15→63.306 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.02 Å2 / Biso mean: 79.3825 Å2 / Biso min: 30.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→63.306 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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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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