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Yorodumi- PDB-5u92: Crystal Structure of arginine kinase from the spider Polybetes py... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u92 | |||||||||||||||||||||||||||
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Title | Crystal Structure of arginine kinase from the spider Polybetes pythagoricus in complex with arginine | |||||||||||||||||||||||||||
Components | arginine kinase | |||||||||||||||||||||||||||
Keywords | TRANSFERASE / arginine kinase / binary complex / spider / Polybetes pythagoricus / phosphagen metabolism | |||||||||||||||||||||||||||
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 | Polybetes pythagoricus (spider) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||||||||||||||||||||
Authors | Lopez-zavala, A.A. / Garcia, C.F. / Paredes-Hernandez, J. / Stojanoff, V. / Sotelo-Mundo, R.R. | |||||||||||||||||||||||||||
Funding support | Mexico, Argentina, United States, 8items
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Citation | Journal: PeerJ / Year: 2017 Title: Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus. Authors: Laino, A. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Carrasco-Miranda, J.S. / Santana, M. / Stojanoff, V. / Sotelo-Mundo, R.R. / Garcia, C.F. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u92.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u92.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 5u92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/5u92 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/5u92 | HTTPS FTP |
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-Related structure data
Related structure data | 5u8eSC 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: 43291.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Polybetes pythagoricus (spider) / Plasmid: PJexpress414 / Details (production host): T7promotor / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: A0A286R7K5*PLUS, arginine kinase | ||
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#2: Chemical | ChemComp-ARG / | ||
#3: Chemical | #4: 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: 2.06 Å3/Da / Density % sol: 40.23 % / Description: large and thin clear plates |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% w/v polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2016 Details: Flat collimating Rh coated mirror, toroidal focussing mirror |
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.181 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.73 Å / Num. obs: 23798 / % possible obs: 99.79 % / Redundancy: 5.5 % / Biso Wilson estimate: 24.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.0703 / Rsym value: 0.0635 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 5.64 / CC1/2: 0.97 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U8E Resolution: 2→19.727 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.27 / 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→19.727 Å
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Refine LS restraints |
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LS refinement shell |
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