+Open data
-Basic information
Entry | Database: PDB / ID: 1rxw | ||||||
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Title | Crystal structure of A. fulgidus FEN-1 bound to DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / helical clamp / helix-3 turn-helix / hydrophobic wedge / 3' flap binding site / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / RNA-DNA hybrid ribonuclease activity / manganese ion binding / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chapados, B.R. / Hosfield, D.J. / Han, S. / Qiu, J. / Yelent, B. / Shen, B. / Tainer, J.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 Title: Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair Authors: Chapados, B.R. / Hosfield, D.J. / Han, S. / Qiu, J. / Yelent, B. / Shen, B. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rxw.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rxw.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rxw_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 1rxw_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 1rxw_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1rxw_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxw ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxw | HTTPS FTP |
-Related structure data
Related structure data | 1rwzC 1rxmC 1rxvSC 1rxzC 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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Details | The biological assembly is a monomer in the asymmetric unit. |
-Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic upstream primer strand |
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#2: DNA chain | Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic upstream primer strand |
#3: Protein | Mass: 38117.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: FEN, AF0264 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29975 |
#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: 2.38 Å3/Da / Density % sol: 48.36 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, ammonium sulfate, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 1999 |
Radiation | Monochromator: Ge(111). conical Si/Rh mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 33233 / Num. obs: 33233 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.056 |
Reflection shell | Resolution: 1.9→1.97 Å / Rsym value: 0.322 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RXV Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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