[English] 日本語
Yorodumi- PDB-2r1l: OpdA from Agrobacterium radiobacter with bound diethyl thiophosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r1l | ||||||
---|---|---|---|---|---|---|---|
Title | OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A | ||||||
Components | Phosphotriesterase | ||||||
Keywords | HYDROLASE / phosphotriesterase / opda / metalloenzyme | ||||||
Function / homology | Function and homology information catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ollis, D.L. / Jackson, C.J. / Foo, J.L. / Kim, H.K. / Carr, P.D. / Liu, J.W. / Salem, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase Authors: Jackson, C.J. / Foo, J.L. / Kim, H.K. / Carr, P.D. / Liu, J.W. / Salem, G. / Ollis, D.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2r1l.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2r1l.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 2r1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/2r1l ftp://data.pdbj.org/pub/pdb/validation_reports/r1/2r1l | HTTPS FTP |
---|
-Related structure data
Related structure data | 2r1kC 2r1mC 2r1nC 2r1pC 3c86C 2d2jS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35674.613 Da / Num. of mol.: 1 / Fragment: UNP residues 32-360 / Mutation: S92A, N265D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: opdA / Plasmid: pCY76 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q93LD7, aryldialkylphosphatase |
---|
-Non-polymers , 5 types, 276 molecules
#2: Chemical | ChemComp-FE2 / |
---|---|
#3: Chemical | ChemComp-CO / |
#4: Chemical | ChemComp-DPJ / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.11 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.2M sodium nitrate, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 24, 2006 / Details: Confocal Mirrors |
Radiation | Monochromator: OSMIC confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 31547 / Num. obs: 31298 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.95→2.07 Å / % possible all: 96.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D2J Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.528 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.12 / 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: 20.31 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
|