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Yorodumi- PDB-6l3p: Crystal strcuture of Feruloyl-CoA hydratase lyase(FCHL) complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l3p | ||||||
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Title | Crystal strcuture of Feruloyl-CoA hydratase lyase(FCHL) complexed with CoA | ||||||
Components | Hydroxycinnamoyl-CoA hydratase-lyase | ||||||
Keywords | LYASE / Feruloyl-CoA hydratae lyase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas putida KT2440 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Seok, J. / Seo, H. / Kim, K.-J. | ||||||
Citation | Journal: to be published Title: Kinetic and structural analysis for bioproduction of vanillin by feruloyl-CoA hydratase/lyase from Pseudomonas putida KT2440 Authors: Seok, J. / Seo, H. / Kim, K.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l3p.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l3p.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 6l3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/6l3p ftp://data.pdbj.org/pub/pdb/validation_reports/l3/6l3p | HTTPS FTP |
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-Related structure data
Related structure data | 6l3oC 2j5iS 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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-Components
#1: Protein | Mass: 32123.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: PP_3358 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q88HJ8, vanillin synthase, trans-feruloyl-CoA hydratase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.4 Å3/Da / Density % sol: 63.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 25% propanediol, PEG3000, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2019 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 29931 / % possible obs: 98.5 % / Redundancy: 11.2 % / CC1/2: 0.995 / Rpim(I) all: 0.022 / Rrim(I) all: 0.084 / Net I/σ(I): 38.3 |
Reflection shell | Resolution: 2.5→2.56 Å / Num. unique obs: 2038 / CC1/2: 0.935 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2j5i Resolution: 2.5→31.52 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.473 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.273 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.06 Å2 / Biso mean: 47.723 Å2 / Biso min: 11.58 Å2
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Refinement step | Cycle: final / Resolution: 2.5→31.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.567 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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