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Yorodumi- PDB-7ews: Crystal structure of arginine kinase (AK3) from the ciliate Param... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ews | ||||||||||||
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Title | Crystal structure of arginine kinase (AK3) from the ciliate Paramecium tetraurelia | ||||||||||||
Components | arginine kinase | ||||||||||||
Keywords | TRANSFERASE / arginine kinase / phosphagen kinase | ||||||||||||
Function / homology | Function and homology information phosphocreatine biosynthetic process / creatine kinase activity / kinase activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Paramecium tetraurelia (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Otsuka, Y. / Yokota, J. / Yano, D. / Uda, K. / Suzuki, T. / Sugiyama, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: To Be Published Title: Crystal structure of arginine kinase (AK3) from the ciliate Paramecium tetraurelia Authors: Otsuka, Y. / Yokota, J. / Yano, D. / Uda, K. / Suzuki, T. / Sugiyama, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ews.cif.gz | 175.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ews.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ews.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/7ews ftp://data.pdbj.org/pub/pdb/validation_reports/ew/7ews | HTTPS FTP |
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-Related structure data
Related structure data | 7egz S: Starting model for refinement |
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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: 45523.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paramecium tetraurelia (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: A0C7I4 #2: Water | ChemComp-HOH / | |
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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: 2.59 Å3/Da / Density % sol: 52.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes-NaOH, pH 7.0, 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.42 Å / Num. obs: 58371 / % possible obs: 99.7 % / Redundancy: 11.8 % / Rrim(I) all: 0.33 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.03→2.17 Å / Num. unique obs: 20108 / CC1/2: 0.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EGZ 7egz Resolution: 2→44.42 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.816 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.165 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.958 Å2
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Refinement step | Cycle: 1 / Resolution: 2→44.42 Å
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Refine LS restraints |
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