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Yorodumi- PDB-4gsi: DNA Holliday junction stabilized by fluorine halogen bond. F2J co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gsi | ||||||
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Title | DNA Holliday junction stabilized by fluorine halogen bond. F2J construct of related reference. | ||||||
Components |
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Keywords | DNA / DNA Holliday junction / halogen bond | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Ho, P.S. / Carter, M. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions. Authors: Carter, M. / Voth, A.R. / Scholfield, M.R. / Rummel, B. / Sowers, L.C. / 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 | 4gsi.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gsi.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 4gsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gsi_validation.pdf.gz | 413.2 KB | Display | wwPDB validaton report |
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Full document | 4gsi_full_validation.pdf.gz | 427.1 KB | Display | |
Data in XML | 4gsi_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 4gsi_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/4gsi ftp://data.pdbj.org/pub/pdb/validation_reports/gs/4gsi | HTTPS FTP |
-Related structure data
Related structure data | 4gqdC 4greC 4gs2C 4gsgC 2orgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3064.968 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence #2: DNA chain | Mass: 3029.994 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetically engineered DNA sequence #3: 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: 2.27 Å3/Da / Density % sol: 63.4 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 7 Details: 0.7mM DNA, 25mM sodium cacodylate pH 7.0 buffer, 10-25mM calcium chloride, and 0.8-1.2mM spermine, equilibrated against a reservoir of 30-40% aqueous MPD, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 133 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Jan 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→55 Å / Num. all: 6763 / Num. obs: 3910 / % possible obs: 24.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066 / Χ2: 5.397 / Net I/σ(I): 23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ORG Resolution: 2.38→32.61 Å / Rfactor Rfree error: 0.022 / Occupancy max: 1 / Occupancy min: 0.4 / Data cutoff high absF: 27432 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 85.8826 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 39.21 Å2 / Biso mean: 15.9929 Å2 / Biso min: 0.11 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.38→32.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.53 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 6
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Xplor file |
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