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- PDB-4mgh: Importance of Hydrophobic Cavities in Allosteric Regulation of Fo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mgh | ||||||
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Title | Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight from Xenon Trapping and Statistical Coupling Analysis | ||||||
![]() | Phosphoribosylformylglycinamidine synthase | ||||||
![]() | LIGASE / Amidotransferasae / Amidotransferase | ||||||
Function / homology | ![]() phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / glutamine metabolic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanwar, A.S. / Goyal, V.D. / Choudhary, D. / Panjikar, S. / Anand, R. | ||||||
![]() | ![]() Title: Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis Authors: Tanwar, A.S. / Goyal, V.D. / Choudhary, D. / Panjikar, S. / Anand, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 278.2 KB | Display | ![]() |
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PDB format | ![]() | 215.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 838.1 KB | Display | ![]() |
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Full document | ![]() | 856 KB | Display | |
Data in XML | ![]() | 50.9 KB | Display | |
Data in CIF | ![]() | 74.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4l78C ![]() 4lgyC ![]() 1t3tS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 142566.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P74881, phosphoribosylformylglycinamidine synthase |
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-Non-polymers , 7 types, 545 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / | ||||||||||
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#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-XE / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M Ammonium Sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 26, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.81738 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→19.99 Å / Num. all: 50158 / Num. obs: 50158 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.067 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 27.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T3T Resolution: 2.65→19.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.46 / SU B: 7.708 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.512 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.53 Å2 / Biso mean: 20.8347 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→19.99 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.65 Å / Total num. of bins used: 20
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