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Yorodumi- PDB-3ia2: Pseudomonas fluorescens esterase complexed to the R-enantiomer of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ia2 | ||||||
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Title | Pseudomonas fluorescens esterase complexed to the R-enantiomer of a sulfonate transition state analog | ||||||
Components | Arylesterase | ||||||
Keywords | HYDROLASE / alpha-beta hydrolase fold / transition state analog / Oxidoreductase / Peroxidase | ||||||
Function / homology | Function and homology information arylesterase / Oxidoreductases / arylesterase activity / peroxidase activity Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Schrag, J.D. / Kazlauskas, R.J. / Jiang, Y. / Morley, K. | ||||||
Citation | Journal: Chembiochem / Year: 2011 Title: Different active-site loop orientation in serine hydrolases versus acyltransferases. Authors: Jiang, Y. / Morley, K.L. / Schrag, J.D. / Kazlauskas, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ia2.cif.gz | 359.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ia2.ent.gz | 293.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ia2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ia2_validation.pdf.gz | 501.5 KB | Display | wwPDB validaton report |
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Full document | 3ia2_full_validation.pdf.gz | 517.6 KB | Display | |
Data in XML | 3ia2_validation.xml.gz | 74.2 KB | Display | |
Data in CIF | 3ia2_validation.cif.gz | 104.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/3ia2 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/3ia2 | HTTPS FTP |
-Related structure data
Related structure data | 1va4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 1 - 271 / Label seq-ID: 1 - 271
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-Components
#1: Protein | Mass: 29993.955 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: pJOE2792 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P22862, arylesterase, Oxidoreductases #2: Chemical | ChemComp-J6Z / ( #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.7 M ammonium sulfate, 3% PEG 400, 100 mM sodium-potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2005 / Details: SI(111) MONOCHROMATOR |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→48.57 Å / Num. all: 373997 / Num. obs: 364141 / % possible obs: 97.4 % / Redundancy: 3.65 % / Rsym value: 0.056 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 3 / Rsym value: 0.343 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VA4 Resolution: 1.65→48.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.712 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 22.959 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→48.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1993 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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