+Open data
-Basic information
Entry | Database: PDB / ID: 6ky3 | ||||||
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Title | Structure of arginine kinase H284A mutant | ||||||
Components | Arginine kinase | ||||||
Keywords | TRANSFERASE / Arginine kinase | ||||||
Function / homology | Function and homology information arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Daphnia magna (crustacean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Rao, Z. / Park, J.H. / Kim, S.Y. / Kim, D.S. | ||||||
Citation | Journal: Mol.Cells / Year: 2020 Title: Insight into Structural Aspects of Histidine 284 of Daphnia magna Arginine Kinase. Authors: Rao, Z. / Kim, S.Y. / Li, X. / Kim, D.S. / Kim, Y.J. / Park, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ky3.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ky3.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ky3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/6ky3 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/6ky3 | HTTPS FTP |
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-Related structure data
Related structure data | 6ky2C 4bhlS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 40587.918 Da / Num. of mol.: 1 / Mutation: H284A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Daphnia magna (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A7CK57 | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ARG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M phosphate buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→46.17 Å / Num. obs: 70591 / % possible obs: 96.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.34→1.41 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 9870 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BHL Resolution: 1.34→46.17 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.34→46.17 Å
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LS refinement shell | Resolution: 1.341→1.376 Å
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