+Open data
-Basic information
Entry | Database: PDB / ID: 6fh2 | ||||||
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Title | Protein arginine kinase McsB in the AMP-PN-bound state | ||||||
Components | Protein-arginine kinase | ||||||
Keywords | SIGNALING PROTEIN / protein kinase / protein arginine kinase / protein arginine phosphorylation / phospho-binding domain | ||||||
Function / homology | Function and homology information protein arginine kinase / phosphocreatine biosynthetic process / creatine kinase activity / protein kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Suskiewicz, M.J. / Heuck, A. / Vu, L.D. / Clausen, T. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2019 Title: Structure of McsB, a protein kinase for regulated arginine phosphorylation. Authors: Suskiewicz, M.J. / Hajdusits, B. / Beveridge, R. / Heuck, A. / Vu, L.D. / Kurzbauer, R. / Hauer, K. / Thoeny, V. / Rumpel, K. / Mechtler, K. / Meinhart, A. / Clausen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fh2.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fh2.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/6fh2 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/6fh2 | HTTPS FTP |
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-Related structure data
Related structure data | 6fh1C 6fh3C 6fh4C 1m15S C: citing same article (ref.) 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
#1: Protein | Mass: 41255.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: mcsB / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DMM5, protein arginine kinase #2: Chemical | ChemComp-AN2 / | #3: Chemical | ChemComp-EDO / #4: 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: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 25% v/v ethylene glycol, 75 mM MES-imidazole, 58 mM sodium formate, 58 mM ammonium acetate, 58 mM sodium citrate, 58 mM sodium potassium tartrate, 58 mM sodium oxamate. Soaked with 10 mM ...Details: 25% v/v ethylene glycol, 75 mM MES-imidazole, 58 mM sodium formate, 58 mM ammonium acetate, 58 mM sodium citrate, 58 mM sodium potassium tartrate, 58 mM sodium oxamate. Soaked with 10 mM magnesium AMPPNP, which apparently hydrolysed during the procedure to ADP. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48 Å / Num. obs: 21210 / % possible obs: 99.76 % / Redundancy: 11.1 % / Biso Wilson estimate: 62.63 Å2 / Net I/σ(I): 15.99 |
Reflection shell | Resolution: 2.7→2.8 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M15 Resolution: 2.7→47.999 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.61 / 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: 2.7→47.999 Å
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Refine LS restraints |
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LS refinement shell |
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