[English] 日本語
Yorodumi- PDB-4cys: G6 mutant of PAS, arylsulfatase from Pseudomonas Aeruginosa, in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cys | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | G6 mutant of PAS, arylsulfatase from Pseudomonas Aeruginosa, in complex with Phenylphosphonic acid | ||||||||||||
Components | ARYLSULFATASE | ||||||||||||
Keywords | HYDROLASE / CATALYTIC PROMISCUITY / DIRECTED EVOLUTION / NEUTRAL DRIFT / SULFATASE / SUPERFAMILY | ||||||||||||
Function / homology | Function and homology information arylsulfatase (type I) / arylsulfatase activity / phosphoric diester hydrolase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||||||||
Authors | Miton, C.M. / Jonas, S. / Mohammed, M.F. / Fischer, G. / Loo, B.v. / Kintses, B. / Hyvonen, M. / Tokuriki, N. / Hollfelder, F. | ||||||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset. Authors: Miton, C.M. / Jonas, S. / Fischer, G. / Duarte, F. / Mohamed, M.F. / van Loo, B. / Kintses, B. / Kamerlin, S.C.L. / Tokuriki, N. / Hyvonen, M. / Hollfelder, F. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cys.cif.gz | 240.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cys.ent.gz | 192.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cys_validation.pdf.gz | 478.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4cys_full_validation.pdf.gz | 490.9 KB | Display | |
Data in XML | 4cys_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 4cys_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/4cys ftp://data.pdbj.org/pub/pdb/validation_reports/cy/4cys | HTTPS FTP |
-Related structure data
Related structure data | 4cxkC 4cxsC 4cxuC 4cyrC 5aj9C 1hdhS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59859.273 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PRSF-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51691, arylsulfatase (type I) |
---|
-Non-polymers , 5 types, 887 molecules
#2: Chemical | #3: Chemical | ChemComp-SV7 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.27 % / Description: NONE |
---|---|
Crystal grow | pH: 6.3 Details: 0.1 M MES PH 6.3, 26.5 % (W/V) PEG 5000 MME, 0.22 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.011 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 2, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.011 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→66.94 Å / Num. obs: 88274 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.88→1.88 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HDH Resolution: 1.88→93.25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.773 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.137 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.773 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→93.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|