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Yorodumi- PDB-1fpq: CRYSTAL STRUCTURE ANALYSIS OF SELENOMETHIONINE SUBSTITUTED CHALCO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fpq | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF SELENOMETHIONINE SUBSTITUTED CHALCONE O-METHYLTRANSFERASE | ||||||
Components | ISOLIQUIRITIGENIN 2'-O-METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / selenomethionine substituted protein | ||||||
Function / homology | Function and homology information isoliquiritigenin 2'-O-methyltransferase / licodione 2'-O-methyltransferase / licodione 2'-O-methyltransferase activity / isoliquiritigenin 2'-O-methyltransferase activity / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Zubieta, C. / Dixon, R.A. / Noel, J.P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases. Authors: Zubieta, C. / He, X.Z. / 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 | 1fpq.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fpq.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fpq ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fpq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer formed by a twofold rotation of the monomer chain A. |
-Components
#1: Protein | Mass: 41881.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Production host: Escherichia coli (E. coli) / References: UniProt: P93324 |
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#2: Chemical | ChemComp-SAM / |
#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: 2.43 Å3/Da / Density % sol: 49.29 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, ammonium acetate, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 1999 | |||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→99 Å / Num. all: 27095 / Num. obs: 27095 / % possible obs: 98 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.9 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.205 / Num. unique all: 2143 / % possible all: 81 | |||||||||||||||||||||||||
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 49336 / Num. measured all: 97770 | |||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 81 % / Mean I/σ(I) obs: 3.7 |
-Processing
Software |
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Refinement | Resolution: 2→32.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2347303.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber Details: F's are averaged from selenomethioine data collected at four wavelengths (SHARP output)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.81 Å2 / ksol: 0.3312 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→32.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.356 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.304 |