+Open data
-Basic information
Entry | Database: PDB / ID: 1fp1 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF CHALCONE O-METHYLTRANSFERASE | ||||||
Components | ISOLIQUIRITIGENIN 2'-O-METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / protein-substrate / protein-product complex | ||||||
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: 1.82 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 | 1fp1.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fp1.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 1fp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fp1_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1fp1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1fp1_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 1fp1_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fp1 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fp1 | 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 the monomer by a two-fold rotation. |
-Components
#1: Protein | Mass: 41178.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Plasmid: PHIS8 / Production host: Escherichia coli (E. coli) / References: UniProt: P93324 |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-HCC / |
#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: 2.46 Å3/Da / Density % sol: 49.96 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, ammonium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
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: BL7-1 / Wavelength: 1.03 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→99 Å / Num. all: 36093 / Num. obs: 32682 / % possible obs: 90.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 2.88 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.82→1.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.66 / Num. unique all: 860 / % possible all: 48.5 |
Reflection | *PLUS Num. measured all: 94322 |
Reflection shell | *PLUS % possible obs: 48 % / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Resolution: 1.82→36.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1481320.39 / 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: 59.48 Å2 / ksol: 0.3777 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.82→36.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.93 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: 38.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.376 / % reflection Rfree: 5.8 % / Rfactor Rwork: 0.352 |