+Open data
-Basic information
Entry | Database: PDB / ID: 1fhy | ||||||||||||||||||
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Title | PSORALEN CROSS-LINKED D(CCGCTAGCGG) FORMS HOLLIDAY JUNCTION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / psoralen / cross-linked DNA / Holliday junction / 4-way junction / DNA-drug complex | Function / homology | 4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | Authors | Eichman, B.F. / Mooers, B.H.M. / Alberti, M. / Hearst, J.E. / Ho, P.S. | Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions. Authors: Eichman, B.F. / Mooers, B.H. / Alberti, M. / Hearst, J.E. / Ho, P.S. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions Authors: Eichman, B.F. / Vargason, J.M. / Mooers, B.H.M. / Ho, P.S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fhy.cif.gz | 21.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fhy.ent.gz | 14.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fhy_validation.pdf.gz | 717 KB | Display | wwPDB validaton report |
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Full document | 1fhy_full_validation.pdf.gz | 720.8 KB | Display | |
Data in XML | 1fhy_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1fhy_validation.cif.gz | 4.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/1fhy ftp://data.pdbj.org/pub/pdb/validation_reports/fh/1fhy | HTTPS FTP |
-Related structure data
Related structure data | 1fhzC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | A four-way junction is a dimer constructed from chains A and B and a symmetry partner generated by the two-fold |
-Components
#1: DNA chain | Mass: 3045.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA IS CROSS-LINKED BY PSORALEN #2: Chemical | ChemComp-PSO / | #3: Chemical | ChemComp-CA / | #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: 2.23 Å3/Da / Density % sol: 44.9 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: sodium cacodylate, MgCl2, MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→34.65 Å / Num. all: 10418 / Num. obs: 2937 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Num. unique all: 299 / % possible all: 99.3 |
Reflection | *PLUS Num. measured all: 10418 |
Reflection shell | *PLUS % possible obs: 99.3 % / Mean I/σ(I) obs: 8.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.65 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson et al. Details: ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→34.65 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 34.7 Å / Rfactor Rfree: 0.283 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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