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Yorodumi- PDB-1uk7: Crystal structure of a meta-cleavage product hydrolase (CumD) com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uk7 | ||||||
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Title | Crystal structure of a meta-cleavage product hydrolase (CumD) complexed with n-butyrate | ||||||
Components | 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase | ||||||
Keywords | HYDROLASE / AROMATIC COMPOUNDS / CUMENE / ISOPROPYLBENZENE / META-CLEAVAGE COMPOUND HYDROLASE / POLYCHLORINATED BIPHENYL DEGRADATION / PSEUDOMONAS FLUORESCENS IP01 / ALPHA/BETA-HYDROLASE / SUBSTRATE SPECIFICITY / CUMENE DEGRADATION / PCB / BETA-KETOLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Fushinobu, S. / Jun, S.-Y. / Hidaka, M. / Nojiri, H. / Yamane, H. / Shoun, H. / Omori, T. / Wakagi, T. | ||||||
Citation | Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 2005 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uk7.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uk7.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1uk7 ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1uk7 | HTTPS FTP |
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-Related structure data
Related structure data | 1uk6C 1uk8C 1uk9C 1ukaC 1ukbC 1iupS 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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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. |
-Components
#1: Protein | Mass: 31506.607 Da / Num. of mol.: 1 / Mutation: S103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: CUMD / Plasmid: PIP140 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P96965, EC: 3.7.1.9 |
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#2: Chemical | ChemComp-BUA / |
#3: 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: 2.51 Å3/Da / Density % sol: 50.54 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: PEG4000, AMMONIUM n-butyrate, SODIUM n-butyrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2002 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.845 Å / Num. all: 38947 / Num. obs: 38090 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.076 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.299 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1IUP Resolution: 1.7→24.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1982617.27 / 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: 43.4517 Å2 / ksol: 0.339624 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→24.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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