+Open data
-Basic information
Entry | Database: PDB / ID: 1p52 | ||||||
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Title | Structure of Arginine kinase E314D mutant | ||||||
Components | Arginine kinase | ||||||
Keywords | TRANSFERASE / ARGININE KINASE / PHOSPHAGEN KINASE / TRANSITION STATE ANALOG / ADENOSINE TRI-PHOSPHATE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Pruett, P.S. / Azzi, A. / Clark, S.A. / Yousef, M.S. / Gattis, J.L. / Somasundarum, T. / Ellington, W.R. / Chapman, M.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The putative catalytic bases have, at most, an accessory role in the mechanism of arginine kinase. Authors: Pruett, P.S. / Azzi, A. / Clark, S.A. / Yousef, M.S. / Gattis, J.L. / Somasundaram, T. / Ellington, W.R. / 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 | 1p52.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p52.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 1p52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p52_validation.pdf.gz | 829.5 KB | Display | wwPDB validaton report |
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Full document | 1p52_full_validation.pdf.gz | 832.6 KB | Display | |
Data in XML | 1p52_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 1p52_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/1p52 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/1p52 | HTTPS FTP |
-Related structure data
Related structure data | 1p50C 1bg0S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40293.766 Da / Num. of mol.: 1 / Mutation: E314D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab) Gene: AK17 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P51541, arginine kinase |
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-Non-polymers , 5 types, 400 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-DAR / | #6: 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: 2.29 Å3/Da / Density % sol: 46.2 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: peg 6000, hEPES, MgCl2, ADP, NO3, ARGININE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: ROTATING ANODE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→10 Å / Num. all: 28834 / Num. obs: 27680 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 17.6 Å2 |
Reflection shell | Resolution: 1.9→2.02 Å / % possible all: 91.6 |
Reflection | *PLUS % possible obs: 98 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.066 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BG0 Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati sigma a free: 0.27 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refinement | *PLUS Highest resolution: 1.9 Å / Rfactor Rwork: 0.181 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |