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- PDB-3ij3: 1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptida... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ij3 | ||||||
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Title | 1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptidase from Coxiella burnetii | ||||||
![]() | Cytosol aminopeptidase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptidase from Coxiella burnetii Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.3 KB | Display | ![]() |
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PDB format | ![]() | 94.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1lamS S: Starting model for refinement |
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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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 53688.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 8 types, 423 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / ![]() | ||||||||||
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#3: Chemical | ChemComp-LI / ![]() | ||||||||||
#4: Chemical | ChemComp-SO4 / ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-PEG / | ![]() #7: Chemical | ![]() #8: Chemical | ![]() #9: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.96 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein solution at 7.0 mg/mL, 0.5M Sodium cloride, Screen solution JCSG+D7, 0.2M Lithium sulfate, 0.1M Tris, 40% v/v PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→30 Å / Num. all: 53424 / Num. obs: 53424 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2656 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1LAM Resolution: 1.8→28.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.861 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Individual Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 15.878 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→28.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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