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Open data
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Basic information
Entry | Database: PDB / ID: 1p50 | ||||||
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Title | Transition state structure of an Arginine Kinase mutant | ||||||
![]() | Arginine kinase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pruett, P.S. / Azzi, A. / Clark, S.A. / Yousef, M.S. / Gattis, J.L. / Somasundarum, T. / Ellington, W.R. / Chapman, M.S. | ||||||
![]() | ![]() 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. #1: ![]() Title: Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.1 KB | Display | ![]() |
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PDB format | ![]() | 64 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1p52C ![]() 1bg0S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 40117.578 Da / Num. of mol.: 1 / Mutation: E103Q, G116A, D112G, E225Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET22b / Species (production host): Escherichia coli / Production host: ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 130 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-ADP / ![]() |
#4: Chemical | ChemComp-NO3 / ![]() |
#5: Chemical | ChemComp-ARG / ![]() |
#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.54 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, Hepes, magnesium chloride, ADP, nitrate, 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 |
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Diffraction source | Source: ![]() | |||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 10, 2000 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: rotating anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection | Resolution: 2.8→10 Å / Num. all: 9424 / Num. obs: 8914 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.128 | |||||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 92 | |||||||||||||||
Reflection | *PLUS % possible obs: 97.4 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1BG0 Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati sigma a free: 0.38 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refinement | *PLUS % reflection Rfree: 3-5 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |