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Yorodumi- PDB-2r1k: OpdA from Agrobacterium radiobacter with bound diethyl phosphate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r1k | ||||||
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Title | OpdA from Agrobacterium radiobacter with bound diethyl phosphate from crystal soaking with the compound- 1.9 A | ||||||
Components | PhosphotriesteraseAryldialkylphosphatase | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r1k.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r1k.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 2r1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/2r1k ftp://data.pdbj.org/pub/pdb/validation_reports/r1/2r1k | HTTPS FTP |
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-Related structure data
Related structure data | 2r1lC 2r1mC 2r1nC 2r1pC 3c86C 2d2jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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 |
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-Non-polymers , 5 types, 294 molecules
#2: Chemical | ChemComp-FE2 / |
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#3: Chemical | ChemComp-CO / |
#4: Chemical | ChemComp-DPF / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.51 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.7385 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 29, 2007 Details: flat collimating mirror, double crystal monochromator, toroid focusing mirror |
Radiation | Monochromator: Osmic confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7385 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 34388 / Num. obs: 33149 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D2J Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.782 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 29.358 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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