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Yorodumi- PDB-4gvy: Crystal structure of arginine kinase in complex with L-citrulline... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gvy | |||||||||
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Title | Crystal structure of arginine kinase in complex with L-citrulline and MgADP | |||||||||
Components | Arginine kinase | |||||||||
Keywords | TRANSFERASE / Arginine kinase / Phosphagen kinase / Transition state analog / Kinase | |||||||||
Function / homology | Function and homology information arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Limulus polyphemus (Atlantic horseshoe crab) | |||||||||
Method | X-RAY DIFFRACTION / ISOMORPHOUS WITH PDB ENTRY 1M15 / Resolution: 2.091 Å | |||||||||
Authors | Clark, S.A. / Davulcu, O. / Chapman, M.S. | |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2012 Title: Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. Authors: Clark, S.A. / Davulcu, O. / Chapman, M.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gvy.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gvy.ent.gz | 125.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/4gvy ftp://data.pdbj.org/pub/pdb/validation_reports/gv/4gvy | HTTPS FTP |
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-Related structure data
Related structure data | 4gvzC 4gw0C 4gw2C 1m15S 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: 40249.758 Da / Num. of mol.: 1 / Mutation: E103N, D112G, G116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab) Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P51541, arginine kinase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-CIR / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.541 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 13, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.091→17.635 Å / Num. all: 20717 / Num. obs: 20717 / % possible obs: 92.14 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.091→2.252 Å / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH PDB ENTRY 1M15 Starting model: PDB ENTRY 1M15 Resolution: 2.091→17.635 Å / SU ML: 0.21 / σ(F): 1 / Phase error: 21.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.164 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.091→17.635 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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