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Yorodumi- PDB-2d2h: OpdA from Agrobacterium radiobacter with bound inhibitor trimethy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d2h | ||||||
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Title | OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution | ||||||
Components | phosphotriesterase | ||||||
Keywords | HYDROLASE / phosphotriesterase / metalloenzyme / OpdA | ||||||
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: 1.8 Å | ||||||
Authors | Jackson, C. / Kim, H.K. / Carr, P.D. / Liu, J.W. / Ollis, D.L. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2005 Title: The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism Authors: Jackson, C. / Kim, H.K. / Carr, P.D. / Liu, J.W. / 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 | 2d2h.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d2h.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 2d2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d2h_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 2d2h_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 2d2h_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 2d2h_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/2d2h ftp://data.pdbj.org/pub/pdb/validation_reports/d2/2d2h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35673.629 Da / Num. of mol.: 1 / Fragment: residues 33-361 / Mutation: S92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: pCY76 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q93LD7, aryldialkylphosphatase | ||||
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#2: Chemical | #3: Chemical | ChemComp-TZZ / | #4: 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: 2.69 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 20% PEG 3350, 0.2M NaNO3, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 12, 2004 / 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: 1.8→20 Å / Num. all: 39806 / Num. obs: 38568 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.6 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.878 / SU B: 1.922 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.116 / 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: 15.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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