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Yorodumi- PDB-6ky2: Crystal Structure of Arginine Kinase wild type from Daphnia magna -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ky2 | ||||||
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Title | Crystal Structure of Arginine Kinase wild type from Daphnia magna | ||||||
Components | Arginine kinase | ||||||
Keywords | TRANSFERASE / Kinase / ATP binding protein / Arginine binding protein | ||||||
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: 1.87 Å | ||||||
Authors | Park, J.H. / Rao, Z. / 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 | 6ky2.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ky2.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ky2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/6ky2 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/6ky2 | HTTPS FTP |
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-Related structure data
Related structure data | 6ky3C 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: 40516.840 Da / Num. of mol.: 1 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 | ChemComp-PO4 / |
#3: 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: 40.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M Phosphate |
-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: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→46.23 Å / Num. obs: 26672 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.87→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.474 / Num. unique obs: 3872 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BHL Resolution: 1.87→46.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.637 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 80.64 Å2 / Biso mean: 26.907 Å2 / Biso min: 11.21 Å2
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Refinement step | Cycle: final / Resolution: 1.87→46.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.872→1.921 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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