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Yorodumi- PDB-7pjo: Crystal form 3 of CPR-C4: a cysteine protease from the Candidate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pjo | ||||||
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Title | Crystal form 3 of CPR-C4: a cysteine protease from the Candidate Phyla Radiation | ||||||
Components | CPR-C4 | ||||||
Keywords | HYDROLASE / cysteine protease | ||||||
Function / homology | PHOSPHATE ION Function and homology information | ||||||
Biological species | Candidate division CPR1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å | ||||||
Authors | Cornish, K.A.S. / Pohl, E. | ||||||
Funding support | European Union, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: CPR-C4 is a highly conserved novel protease from the Candidate Phyla Radiation with remote structural homology to human vasohibins. Authors: Cornish, K.A.S. / Lange, J. / Aevarsson, A. / Pohl, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pjo.cif.gz | 188 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pjo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/7pjo ftp://data.pdbj.org/pub/pdb/validation_reports/pj/7pjo | HTTPS FTP |
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-Related structure data
Related structure data | 7ob6SC 7ob7C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 27331.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidate division CPR1 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express #2: Chemical | ChemComp-PO4 / #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: 2.57 Å3/Da / Density % sol: 52.11 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / Details: Lithium sulfate, Tris, PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 27, 2021 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.248→44.302 Å / Num. obs: 27119 / % possible obs: 98.1 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 17.1 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7OB6 Resolution: 2.248→44.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.2 / SU ML: 0.149 / Cross valid method: FREE R-VALUE / ESU R: 0.24 / ESU R Free: 0.196 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.088 Å2
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Refinement step | Cycle: LAST / Resolution: 2.248→44.26 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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