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- PDB-2d0d: Crystal Structure of a Meta-cleavage Product Hydrolase (CumD) A12... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2d0d | ||||||
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Title | Crystal Structure of a Meta-cleavage Product Hydrolase (CumD) A129V Mutant | ||||||
![]() | 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase | ||||||
![]() | HYDROLASE / alpha/beta-hydrolase / beta-ketolase / meta-cleavage product hydrolase / substrate specificity / cumene degradation / polychlorinated biphenyl degradation / PCB | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jun, S.Y. / Fushinobu, S. / Nojiri, H. / Omori, T. / Shoun, H. / Wakagi, T. | ||||||
![]() | ![]() Title: Improving the catalytic efficiency of a meta-cleavage product hydrolase (CumD) from Pseudomonas fluorescens IP01 Authors: Jun, S.Y. / Fushinobu, S. / Nojiri, H. / Omori, T. / Shoun, H. / Wakagi, T. #1: ![]() Title: A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products Authors: Fushinobu, S. / Jun, S.Y. / Hidaka, M. / Nojiri, H. / Yamane, H. / Shoun, H. / Omori, T. / Wakagi, T. #2: ![]() Title: Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products Authors: Fushinobu, S. / Saku, T. / Hidaka, M. / Jun, S.Y. / Nojiri, H. / Yamane, H. / Shoun, H. / Omori, T. / Wakagi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.6 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.4 KB | Display | ![]() |
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Full document | ![]() | 437.9 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iupS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: x, -y+1, -z. |
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Components
#1: Protein | Mass: 31550.658 Da / Num. of mol.: 1 / Mutation: A129V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: PEG 3000, sodium phosphate/citrate, sodium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2004 |
Radiation | Monochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.84 Å / Num. all: 42760 / Num. obs: 42732 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.062 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.65→1.71 Å / Mean I/σ(I) obs: 5.5 / Num. unique all: 4242 / Rsym value: 0.237 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IUP Resolution: 1.65→46.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1954847.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.0574 Å2 / ksol: 0.343085 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→46.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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