[English] 日本語
Yorodumi- PDB-2bje: Acylphosphatase from Sulfolobus solfataricus. Monclinic P21 space... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bje | ||||||
---|---|---|---|---|---|---|---|
Title | Acylphosphatase from Sulfolobus solfataricus. Monclinic P21 space group | ||||||
Components | ACYLPHOSPHATASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rosano, C. / Zuccotti, S. | ||||||
Citation | Journal: Proteins: Struct., Funct., Bioinf. / Year: 2006 Title: Structure, Conformational Stability, and Enzymatic Properties of Acylphosphatase from the Hyperthermophile Sulfolobus Solfataricus. Authors: Corazza, A. / Rosano, C. / Pagano, K. / Alverdi, V. / Esposito, G. / Capanni, C. / Bemporad, F. / Plakoutsi, G. / Stefani, M. / Chiti, F. / Zuccotti, S. / Bolognesi, M. / Viglino, P. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Preliminary Characterization of Two Different Crystal Forms of Acylphosphatase from the Hyperthermophile Archaeon Sulfolobus Solfataricus Authors: Zuccotti, S. / Rosano, C. / Bemporad, F. / Stefani, M. / Bolognesi, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bje.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bje.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/2bje ftp://data.pdbj.org/pub/pdb/validation_reports/bj/2bje | HTTPS FTP |
---|
-Related structure data
Related structure data | 1y9oC 2bjdC 2acyS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11652.300 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97ZL0, acylphosphatase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 33.65 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.54 Å / Num. obs: 25338 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 / % possible all: 95.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ACY Resolution: 1.9→8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.231 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.37 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|