+Open data
-Basic information
Entry | Database: PDB / ID: 1iq6 | ||||||
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Title | (R)-HYDRATASE FROM A. CAVIAE INVOLVED IN PHA BIOSYNTHESIS | ||||||
Components | (R)-SPECIFIC ENOYL-COA HYDRATASE | ||||||
Keywords | LYASE / hydratase / (R)-hydratase / enoyl-CoA hydratase / polyhydroxyalkanoate / Aeromonas caviae / the hydratase 2 motif | ||||||
Function / homology | Function and homology information enoyl-CoA hydratase 2 / fatty acid synthase complex / : / fatty acid synthase activity / fatty acid biosynthetic process / lyase activity Similarity search - Function | ||||||
Biological species | Aeromonas punctata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å | ||||||
Authors | Hisano, T. / Tsuge, T. / Fukui, T. / Iwata, T. / Doi, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of the (R)-specific enoyl-CoA hydratase from Aeromonas caviae involved in polyhydroxyalkanoate biosynthesis Authors: Hisano, T. / Tsuge, T. / Fukui, T. / Iwata, T. / Miki, K. / Doi, Y. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF (R)-SPECIFIC ENOYL-COA HYDRATASE FROM AEROMONAS CAVIAE INVOLVED IN POLYHYDROXYALKANOATE BIOSYNTHESIS Authors: Hisano, T. / Fukui, T. / Iwata, T. / Doi, Y. #2: Journal: J.BACTERIOL. / Year: 1998 Title: EXPRESSION AND CHARACTERIZATION OF (R)-SPECIFIC ENOYL-COA HYDRATASE INVOLVED IN POLYHYDROXYALKANOATE BIOSYNTHESIS BY AEROMONAS CAVIAE Authors: Fukui, T. / SHIOMI, N. / Doi, Y. #3: Journal: J.BACTERIOL. / Year: 1997 Title: CLONING AND ANALYSIS OF THE POLY(3-HYDROXYBUTYRATE-CO-3-HYDROXYHEXANOATE) BIOSYNTHESIS GENES OF AEROMONAS CAVIAE Authors: Fukui, T. / Doi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iq6.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iq6.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 1iq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iq6_validation.pdf.gz | 378.7 KB | Display | wwPDB validaton report |
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Full document | 1iq6_full_validation.pdf.gz | 380.1 KB | Display | |
Data in XML | 1iq6_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1iq6_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iq6 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iq6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14099.186 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas punctata (bacteria) / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32472, enoyl-CoA hydratase #2: Chemical | ChemComp-IPA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 % Description: THE INITIAL STRUCTURE WAS DETERMINED AT 3.0 A RESOLUTION BY MIRAS WITH NATIVE DATA AND THREE SETS OF DERIVATIVE DATA, ALL OF WHICH WERE COLLECTED AT ROOM TEMPERATURE WITH A ROTATING ...Description: THE INITIAL STRUCTURE WAS DETERMINED AT 3.0 A RESOLUTION BY MIRAS WITH NATIVE DATA AND THREE SETS OF DERIVATIVE DATA, ALL OF WHICH WERE COLLECTED AT ROOM TEMPERATURE WITH A ROTATING ANODE X-RAY GENERATOR. THIS MODEL WAS USED TO PHASE THE 1.5 A DATA COLLECTED AT 100K WITH SYNCHROTRON RADIATION BY MOLECULAR REPLACEMENT, AND REFINED BY MOLECULAR DYNAMICS SIMULATION. | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG4000, HEPES, ISOPROPANOL, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 52985 / % possible obs: 99.4 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.052 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 52985 / % possible obs: 99.4 % / Num. measured all: 198695 / Rmerge(I) obs: 0.052 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: A STRUCTURE OF (R)-HYDRATASE FROM A.CAVIAE DETERMINED BY MIRAS AT 3.0 A RESOLUTION Resolution: 1.5→19.15 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.65 Å2 / ksol: 0.43 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 19.15 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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