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- PDB-4lgy: 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: 4lgy | ||||||
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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 / Amido transferase | ||||||
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 | ![]() | 320.7 KB | Display | ![]() |
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PDB format | ![]() | 245.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 853.6 KB | Display | ![]() |
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Full document | ![]() | 905.1 KB | Display | |
Data in XML | ![]() | 68.9 KB | Display | |
Data in CIF | ![]() | 106.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4l78C ![]() 4mghC ![]() 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: 142777.594 Da / Num. of mol.: 1 / Mutation: F209W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P74881, phosphoribosylformylglycinamidine synthase |
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-Non-polymers , 7 types, 1650 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / | ||||||||||
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#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.65 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97372 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→27.5 Å / Num. all: 274143 / Num. obs: 274143 / % possible obs: 96.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.3 |
Reflection shell | Highest resolution: 1.48 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T3T Resolution: 1.48→27.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 0.749 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.885 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→27.5 Å
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Refine LS restraints |
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