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Yorodumi- PDB-4b9e: Structure of a putative epoxide hydrolase from Pseudomonas aerugi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b9e | ||||||
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Title | Structure of a putative epoxide hydrolase from Pseudomonas aeruginosa, with bound MFA. | ||||||
Components | PROBABLE EPOXIDE HYDROLASE | ||||||
Keywords | HYDROLASE / MONOFLUOROACETATE / DEFLUORINASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Schmidberger, J.W. / Schnell, R. / Schneider, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery. Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / Naismith, J.H. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b9e.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b9e.ent.gz | 121.3 KB | Display | PDB format |
PDBx/mmJSON format | 4b9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/4b9e ftp://data.pdbj.org/pub/pdb/validation_reports/b9/4b9e | HTTPS FTP |
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-Related structure data
Related structure data | 2xu8C 4avfC 4avrC 4avyC 4b79C 4b7cC 4b7xC 4b9aC 4es6C 4etrC 4exaC 4exbC 1y37S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33615.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9I229 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | CLONING AND CLEAVAGE OF THE HIS TAG LEFT AND EXTRA N- TERMINAL SERINE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.5 % Description: BEING A SOAK EXPERIMENT, THIS DATA WAS ACTUALLY REFINED AGAINST THE NATIVE UNLIGANDED STRUCTURE WITH PDB CODE 4B9A. |
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Crystal grow | pH: 8.5 Details: 0.1 M LI2SO4, 1.25 M (NH4)2SO4, 0.1 M TRIS HCL PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0064 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0064 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→36.83 Å / Num. obs: 99408 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y37 Resolution: 1.4→36.27 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.143 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / 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: 17.522 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→36.27 Å
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Refine LS restraints |
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