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- PDB-1f52: CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f52 | ||||||
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Title | CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM CO-CRYSTALLIZED WITH ADP | ||||||
Components | GLUTAMINE SYNTHETASE | ||||||
Keywords | LIGASE / glutamine synthetase / ADP / MPD | ||||||
Function / homology | Function and homology information nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / protein homooligomerization / manganese ion binding / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Gill, H.S. / Pfluegl, G.M.U. / Eisenberg, D. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition. Authors: Gill, H.S. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f52.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1f52.ent.gz | 950.6 KB | Display | PDB format |
PDBx/mmJSON format | 1f52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f52_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 1f52_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 1f52_validation.xml.gz | 281.8 KB | Display | |
Data in CIF | 1f52_validation.cif.gz | 372.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/1f52 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/1f52 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological complex is a dodecamer. |
-Components
#1: Protein | Mass: 51744.418 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Description: BACTERIA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1P6, glutamine synthetase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ADP, MPD, spermine, manganese chloride, imidazole buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→34.9 Å / Num. all: 196561 / Num. obs: 196561 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2.49→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.133 / Num. unique all: 8787 / % possible all: 87.8 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→34.9 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The model was refined using strict 12-fold NCS-averaging, i.e. constraints. The 2-methyl-2,4-pentanediol (MPD) molecules were restrained to match PDB code 3AL1. A bulk solvent correction was ...Details: The model was refined using strict 12-fold NCS-averaging, i.e. constraints. The 2-methyl-2,4-pentanediol (MPD) molecules were restrained to match PDB code 3AL1. A bulk solvent correction was applied to the data set. Method Used: J.-S. Jiang and A.T. Brunger, J. Mol. Biol. 243, 100-115 (1994).
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Displacement parameters | Biso mean: 55.54 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.49→34.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | |||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: parhcsdx.pro / Topol file: tophcsdx.pro | |||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 34.9 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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