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Yorodumi- PDB-7qst: Crystal structure of homing endonuclease-associated PhoVMA intein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qst | |||||||||
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Title | Crystal structure of homing endonuclease-associated PhoVMA intein (C1A) | |||||||||
Components | V-type ATP synthase subunit A | |||||||||
Keywords | HYDROLASE / intein / protein splicing / endonuclease | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | |||||||||
Authors | Beyer, H.M. / Iwai, H. | |||||||||
Funding support | Denmark, 2items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Structural Basis for the Propagation of Homing Endonuclease-Associated Inteins. Authors: Beyer, H.M. / Iwai, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qst.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qst.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 7qst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qst_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 7qst_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 7qst_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 7qst_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/7qst ftp://data.pdbj.org/pub/pdb/validation_reports/qs/7qst | HTTPS FTP |
-Related structure data
Related structure data | 7qssC 7qsuC 2cw7S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 42583.168 Da / Num. of mol.: 1 / Mutation: C1A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: HA331_07965 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832T7H1 | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM HEPES pH 8.0, 5 mM cadmium chloride, 5 mM magnesium chloride, 5 mM nickel (II) chloride, 10% (w/v) polyethylene glycol (PEG) 3350 |
-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 PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→43.54 Å / Num. obs: 16191 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 65.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.714 / Net I/σ(I): 17.28 |
Reflection shell | Resolution: 2.49→2.64 Å / Num. unique obs: 2599 / CC1/2: 0.874 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2cw7 Resolution: 2.49→43.51 Å / SU ML: 0.3837 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.4004 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 81.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→43.51 Å
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Refine LS restraints |
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LS refinement shell |
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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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