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- PDB-4oj3: The crystal structure of V84P mutant of S. solfataricus Acylphosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4oj3 | ||||||
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Title | The crystal structure of V84P mutant of S. solfataricus Acylphosphatase | ||||||
![]() | Acylphosphatase | ||||||
![]() | HYDROLASE / native-like aggregation / amyloid aggregation / acylphosphatase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Rosa, M. / Bolognesi, M. / Ricagno, S. | ||||||
![]() | ![]() Title: Edge strand engineering prevents native-like aggregation in Sulfolobus solfataricus acylphosphatase. Authors: de Rosa, M. / Bemporad, F. / Pellegrino, S. / Chiti, F. / Bolognesi, M. / Ricagno, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.1 KB | Display | ![]() |
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PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.3 KB | Display | ![]() |
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Full document | ![]() | 457 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ojgC ![]() 4ojhC ![]() 4oixS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 11650.283 Da / Num. of mol.: 2 / Mutation: V84 to Pro Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M ammonium sulphate, 25% PEG 4K, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2013 / Details: Pt coated mirrors |
Radiation | Monochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30.48 Å / Num. obs: 9635 / % possible obs: 93.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1400 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OIX Resolution: 2.2→30.5 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.837 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.248 / 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: 26.347 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 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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