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Yorodumi- PDB-8cpo: Crystal structure of the PolB16_OarG intein variant S1A, N183A, C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cpo | ||||||
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Title | Crystal structure of the PolB16_OarG intein variant S1A, N183A, C111A, C165A | ||||||
Components | PolB16 Intein Cys-less | ||||||
Keywords | SPLICING / split intein / ligation / protein engineering | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kattelmann, S. / Pasch, T. / Mootz, H.D. / Kuemmel, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Chem Sci / Year: 2023 Title: Structural and biochemical analysis of a novel atypically split intein reveals a conserved histidine specific to cysteine-less inteins. Authors: Pasch, T. / Schroder, A. / Kattelmann, S. / Eisenstein, M. / Pietrokovski, S. / Kummel, D. / Mootz, H.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cpo.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cpo.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/8cpo ftp://data.pdbj.org/pub/pdb/validation_reports/cp/8cpo | HTTPS FTP |
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-Related 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: 23433.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) |
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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: 2.31 Å3/Da / Density % sol: 46.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Phosphate/citrate pH 4.2, 38% EtOH 5% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.976252 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976252 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 7009 / % possible obs: 99.6 % / Redundancy: 19.2 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 37.59 |
Reflection shell | Resolution: 2.6→2.75 Å / Num. unique obs: 1109 / CC1/2: 0.96 / Rrim(I) all: 0.975 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.634 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.03 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→47.634 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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