+Open data
-Basic information
Entry | Database: PDB / ID: 7vcj | ||||||
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Title | Arginine kinase H227A from Daphnia magna | ||||||
Components | Arginine kinase | ||||||
Keywords | TRANSFERASE / Arginine Kinase / Stability / secondary structure | ||||||
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: 1.75 Å | ||||||
Authors | Kim, D.S. / Jang, K. / Kim, W.S. / Kim, Y.J. / Park, J.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Molecules / Year: 2022 Title: Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability. Authors: Kim, D.S. / Jang, K. / Kim, W.S. / Ryu, M. / Park, J.H. / Kim, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vcj.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vcj.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/7vcj ftp://data.pdbj.org/pub/pdb/validation_reports/vc/7vcj | HTTPS FTP |
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-Related structure data
Related structure data | 6ky2S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40378.695 Da / Num. of mol.: 1 / Mutation: H227A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Daphnia magna (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A7CK57, arginine kinase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-NO3 / |
#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: 2.06 Å3/Da / Density % sol: 40.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M Sodium/Potassium phosphate, pH 8.17 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.4 Å / Num. obs: 33113 / % possible obs: 98.43 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.75→1.77 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 31495 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KY2 Resolution: 1.75→38.42 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.88 / 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: 1.75→38.42 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -4.9143 Å / Origin y: 6.1573 Å / Origin z: 16.9643 Å
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Refinement TLS group | Selection details: all |