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Yorodumi- PDB-1kyw: Crystal Structure Analysis of Caffeic Acid/5-hydroxyferulic acid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kyw | ||||||
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Title | Crystal Structure Analysis of Caffeic Acid/5-hydroxyferulic acid 3/5-O-methyltransferase in complex with 5-hydroxyconiferaldehyde | ||||||
Components | Caffeic acid 3-O-methyltransferase | ||||||
Keywords | TRANSFERASE / O-methyltransferase / lignification / protein-ligand complex | ||||||
Function / homology | Function and homology information caffeate O-methyltransferase activity / caffeate O-methyltransferase / phenylpropanoid biosynthetic process / lignin biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Zubieta, C. / Kota, P. / Ferrer, J.-L. / Dixon, R.A. / Noel, J.P. | ||||||
Citation | Journal: Plant Cell / Year: 2002 Title: Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase. Authors: Zubieta, C. / Kota, P. / Ferrer, J.L. / Dixon, R.A. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kyw.cif.gz | 219.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kyw.ent.gz | 175.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kyw_validation.pdf.gz | 957.2 KB | Display | wwPDB validaton report |
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Full document | 1kyw_full_validation.pdf.gz | 1003.4 KB | Display | |
Data in XML | 1kyw_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 1kyw_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/1kyw ftp://data.pdbj.org/pub/pdb/validation_reports/ky/1kyw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39990.098 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Production host: Escherichia coli (E. coli) / References: UniProt: P28002, caffeate O-methyltransferase #2: Chemical | #3: Chemical | #4: 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: 2.82 Å3/Da / Density % sol: 56.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, calcium actetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 13, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→90 Å / Num. all: 52828 / Num. obs: 47650 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 30.6 Å2 |
Reflection shell | Resolution: 2.38→2.42 Å / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2 / Rsym value: 0.557 / % possible all: 43.7 |
Reflection | *PLUS Lowest resolution: 90 Å / Num. obs: 53959 / % possible obs: 89 % / Num. measured all: 207847 / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS % possible obs: 43 % / Rmerge(I) obs: 0.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: partial seleno-methionine model of COMT (unpublished) Resolution: 2.4→97.36 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1028582.19 / 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: 48.3534 Å2 / ksol: 0.361262 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→97.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.205 / Highest resolution: 2.4 Å / Lowest resolution: 99 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.384 / Rfactor Rwork: 0.316 |