+Open data
-Basic information
Entry | Database: PDB / ID: 1fp2 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF ISOFLAVONE O-METHYLTRANSFERASE | ||||||
Components | ISOFLAVONE O-METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / protein-product complex | ||||||
Function / homology | Function and homology information isoflavone 7-O-methyltransferase / isoflavone 7-O-methyltransferase activity / : / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 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 | 1fp2.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fp2.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fp2_validation.pdf.gz | 970.4 KB | Display | wwPDB validaton report |
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Full document | 1fp2_full_validation.pdf.gz | 977.7 KB | Display | |
Data in XML | 1fp2_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 1fp2_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fp2 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fp2 | HTTPS FTP |
-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 constructed from chain A by a two-fold rotation. |
-Components
#1: Protein | Mass: 39648.715 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: O24529 |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-HMO / |
#4: 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: 2.83 Å3/Da / Density % sol: 56.61 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.25 Details: PEG 8000, lithium sulfate, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→99 Å / Num. all: 87599 / Num. obs: 82735 / % possible obs: 94.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 1.8 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.65 / Num. unique all: 6859 / % possible all: 65.5 |
Reflection | *PLUS Num. measured all: 152679 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 65 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.3 |
-Processing
Software |
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Refinement | Resolution: 1.4→69.71 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1360469.45 / 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.34 Å2 / ksol: 0.3714 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→69.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.017 / 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 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.413 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.37 |