+Open data
-Basic information
Entry | Database: PDB / ID: 1va4 | ||||||
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Title | Pseudomonas fluorescens aryl esterase | ||||||
Components | Arylesterase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / esterase / non-cofactor dependent haloperoxidase | ||||||
Function / homology | Function and homology information arylesterase / Oxidoreductases / peroxidase activity / arylesterase activity Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.804 Å | ||||||
Authors | Cheeseman, J.D. / Tocilj, A. / Park, S. / Schrag, J.D. / Kazlauskas, R.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of an aryl esterase from Pseudomonas fluorescens. Authors: Cheeseman, J.D. / Tocilj, A. / Park, S. / 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 | 1va4.cif.gz | 349.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1va4.ent.gz | 284.4 KB | Display | PDB format |
PDBx/mmJSON format | 1va4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1va4 ftp://data.pdbj.org/pub/pdb/validation_reports/va/1va4 | HTTPS FTP |
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-Related structure data
Related structure data | 1a8sS 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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-Components
#1: Protein | Mass: 30966.955 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SIK WI / Plasmid: pUE1251 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P22862, arylesterase #2: Chemical | ChemComp-GOL / #3: 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: 4.3 Å3/Da / Density % sol: 71.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1% PEG 400, 1.65M (NH4)2SO4, 0.1M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 15, 2003 / Details: Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.8 Å / Num. all: 285139 / Num. obs: 271452 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.04 % / Rsym value: 0.066 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.804→1.851 Å / Redundancy: 2.43 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1314 / Rsym value: 0.247 / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A8S Resolution: 1.804→48.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.77 / SU ML: 0.052 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.09 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.672 Å2
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Refinement step | Cycle: LAST / Resolution: 1.804→48.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.804→1.851 Å / Total num. of bins used: 20 /
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