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Yorodumi- PDB-4bb0: Structure of a putative epoxide hydrolase Q244E mutant from Pseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bb0 | ||||||
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Title | Structure of a putative epoxide hydrolase Q244E mutant from Pseudomonas aeruginosa, with bound MFA. | ||||||
Components | PROBABLE EPOXIDE HYDROLASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Schmidberger, J.W. / Schnell, R. / Schneider, G. | ||||||
Citation | Journal: To be Published Title: Structure of a Putative Epoxide Hydrolase Mutant Authors: Schmidberger, J.W. / Schnell, R. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bb0.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bb0.ent.gz | 115.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bb0_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 4bb0_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 4bb0_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 4bb0_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/4bb0 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/4bb0 | HTTPS FTP |
-Related structure data
Related structure data | 4b9aS 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: 33616.965 Da / Num. of mol.: 1 / Mutation: YES 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 | ChemComp-SO4 / #3: Chemical | ChemComp-FAH / #4: Water | ChemComp-HOH / | Nonpolymer details | MONOFLUORO | Sequence details | CLONING AND CUTTING OF THE HIS TAG LEAVES AND EXTRA N- TERMINAL SERINE. THIS MODEL IS A Q244E MUTANT. | |
-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: THIS MODEL WAS ACTUALLY SOLVED BY REFINING THE DATA AGAINST THE NATIVE MODEL OF PA2086 USING REFMAC. |
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Crystal grow | pH: 8.5 Details: 0.1 M LI2 SO4, 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: MAX II / Beamline: I911-3 / Wavelength: 1.04088 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04088 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→29.15 Å / Num. obs: 48281 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4B9A Resolution: 1.77→27.16 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.43 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 24.335 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→27.16 Å
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Refine LS restraints |
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