+Open data
-Basic information
Entry | Database: PDB / ID: 5c8v | ||||||
---|---|---|---|---|---|---|---|
Title | Lucilia cuprina alpha esterase 7: Gly137Asp | ||||||
Components | Carboxylic ester hydrolaseCarboxylesterase | ||||||
Keywords | HYDROLASE / Acetylcholinesterase / Animals / Australia / Carboxylesterase / Catalytic Domain / Diptera / Drug Resistance / Genes / Insect / Insecticides / Phosphorylation / Protein Structure / Sheep / Sheep Diseases / Substrate Specificity | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity Similarity search - Function | ||||||
Biological species | Lucilia cuprina (Australian sheep blowfly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Correy, G.J. / Mabbitt, P.D. / Jackson, C.J. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Conformational Disorganization within the Active Site of a Recently Evolved Organophosphate Hydrolase Limits Its Catalytic Efficiency. Authors: Mabbitt, P.D. / Correy, G.J. / Meirelles, T. / Fraser, N.J. / Coote, M.L. / Jackson, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5c8v.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5c8v.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 5c8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/5c8v ftp://data.pdbj.org/pub/pdb/validation_reports/c8/5c8v | HTTPS FTP |
---|
-Related structure data
Related structure data | 4fngS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 65486.797 Da / Num. of mol.: 1 Mutation: D83A, G137D, M364L, I419F, A472T, I505T, K530E, D554G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lucilia cuprina (Australian sheep blowfly) Gene: LcaE7 / Production host: Escherichia coli (E. coli) References: UniProt: Q25252, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.92 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium-acetate (pH 4.6) and 20% PEG 2K MME / PH range: 4.0-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.8726 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→56.37 Å / Num. obs: 44051 / % possible obs: 95.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.01→2.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 1.4 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FNG Resolution: 2.01→56.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.929 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.187 / 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: 27.203 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.01→56.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|