[English] 日本語
Yorodumi- PDB-4lgy: Importance of Hydrophobic Cavities in Allosteric Regulation of Fo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lgy | ||||||
---|---|---|---|---|---|---|---|
Title | Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight from Xenon Trapping and Statistical Coupling Analysis | ||||||
Components | Phosphoribosylformylglycinamidine synthase | ||||||
Keywords | LIGASE / Amido transferase | ||||||
Function / homology | Function and homology information 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 | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Tanwar, A.S. / Goyal, V.D. / Choudhary, D. / Panjikar, S. / Anand, R. | ||||||
Citation | Journal: Plos One / Year: 2013 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lgy.cif.gz | 320.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lgy.ent.gz | 245.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/4lgy ftp://data.pdbj.org/pub/pdb/validation_reports/lg/4lgy | HTTPS FTP |
---|
-Related structure data
Related structure data | 4l78C 4mghC 1t3tS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Production host: Escherichia coli (E. coli) References: UniProt: P74881, phosphoribosylformylglycinamidine synthase |
---|
-Non-polymers , 7 types, 1650 molecules
#2: Chemical | ChemComp-ADP / | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.65 % |
---|---|
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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97372 Å |
---|---|
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→27.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|