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Yorodumi- PDB-4oix: Crystal structure of truncated Acylphosphatase from S. sulfataricus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oix | ||||||
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Title | Crystal structure of truncated Acylphosphatase from S. sulfataricus | ||||||
Components | Acylphosphatase | ||||||
Keywords | HYDROLASE / native-like aggregation / acylphosphatase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Dilovic, I. / Bolognesi, M. / Ricagno, S. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of truncated Acylphosphatase from S. sulfataricus Authors: Dilovic, I. / Bolognesi, M. / Ricagno, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oix.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oix.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 4oix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/4oix ftp://data.pdbj.org/pub/pdb/validation_reports/oi/4oix | HTTPS FTP |
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-Related structure data
Related structure data | 4oj1C 2bjeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11652.300 Da / Num. of mol.: 1 / Fragment: Delta-11 AcP Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: acyP, SSO0887 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97ZL0, acylphosphatase |
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#2: 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: 1.73 Å3/Da / Density % sol: 28.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% PEG 8000, 8% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0716 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2013 / Details: bent collimating mirror and toroid |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0716 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→31.78 Å / Num. all: 12271 / Num. obs: 11780 / % possible obs: 96 % / Redundancy: 4.7 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 10.7 / Num. unique all: 1398 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2BJE Resolution: 1.55→28.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.581 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.079 / 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: 14.493 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→28.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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