[English] 日本語
Yorodumi- PDB-1iun: meta-Cleavage product hydrolase from Pseudomonas fluorescens IP01... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iun | ||||||
---|---|---|---|---|---|---|---|
Title | meta-Cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) S103A mutant hexagonal | ||||||
Components | meta-Cleavage product 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fushinobu, S. / Saku, T. / Hidaka, M. / Jun, S.-Y. / Nojiri, H. / Yamane, H. / Shoun, H. / Omori, T. / Wakagi, T. | ||||||
Citation | Journal: PROTEIN SCI. / Year: 2002 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. #1: Journal: J.Biosci.Bioeng. / Year: 2002 Title: Purification, characterization, and steady-state kinetics of a meta-cleavage compound hydrolase from Pseudomonas fluorescens IP01 Authors: Saku, T. / Fushinobu, S. / Jun, S.-Y. / Ikeda, N. / Nojiri, H. / Yamane, H. / Omori, T. / Wakagi, T. #2: Journal: Appl.Environ.Microbiol. / Year: 1996 Title: Analysis of cumene (isopropylbenzene) degradation genes from Pseudomonas fluorescens IP01 Authors: Habe, H. / Kasuga, K. / Nojiri, H. / Yamane, H. / Omori, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1iun.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1iun.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 1iun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iun_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1iun_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 1iun_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 1iun_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/1iun ftp://data.pdbj.org/pub/pdb/validation_reports/iu/1iun | HTTPS FTP |
-Related structure data
Related structure data | 1iuoC 1iupC 1c4xS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer in the asymmetric unit |
-Components
#1: Protein | Mass: 31506.607 Da / Num. of mol.: 2 / Mutation: S103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: IP01 / Gene: cumD / Plasmid: pIP140 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P96965, EC: 3.7.1.9 #2: Chemical | ChemComp-ACT / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.15 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: PEG4000, ammonium acetate, sodium acetate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 4, 1999 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 21101 / Num. obs: 21088 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2041 / Rsym value: 0.299 / % possible all: 97.1 |
Reflection | *PLUS Num. obs: 21101 / Num. measured all: 128777 / Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 97.1 % / Rmerge(I) obs: 0.299 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C4X Resolution: 2.8→49.78 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: No NCS restrain at last
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3322 Å2 / ksol: 0.333173 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.53 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 49.8 Å / % reflection Rfree: 5 % / Rfactor all: 0.1988 / Rfactor obs: 0.1988 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.356 / Rfactor Rwork: 0.277 |