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- PDB-3sd7: 1.7 Angstrom Resolution Crystal Structure of Putative Phosphatase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3sd7 | ||||||
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Title | 1.7 Angstrom Resolution Crystal Structure of Putative Phosphatase from Clostridium difficile | ||||||
![]() | Putative phosphatase![]() | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 1.7 Angstrom Resolution Crystal Structure of Putative Phosphatase from Clostridium difficile. Authors: Minasov, G. / 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 | ![]() | 107.7 KB | Display | ![]() |
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PDB format | ![]() | 87.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 311.1 KB | Display | ![]() |
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Full document | ![]() | 314 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mc1S 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 27815.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 166 molecules 








#2: Chemical | ChemComp-NA / | ||
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#3: Chemical | ChemComp-CL / ![]() | ||
#4: Chemical | ChemComp-PGE / ![]() | ||
#5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein: 7.1mG/mL, 0.5M Sodium chloride, 0.01M Tris, pH 8.3, Screen: JCSG+, D12, 0.04M Potassium Phosphate, 16% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 2011 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→30 Å / Num. all: 26648 / Num. obs: 26648 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1216 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3MC1 Resolution: 1.7→29.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.094 / SU ML: 0.062 Isotropic thermal model: Thermal Factors Individually Refined Cross valid method: THROUGHOUT / ESU R: 0.1 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 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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