+Open data
-Basic information
Entry | Database: PDB / ID: 1rxv | ||||||
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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 / 3' flap binding site / protein-dna complex / dna repair / dna replication / 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: 2.5 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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Remark 999 | SEQUENCE Authors also crystallized the sequence CGATGCTA, however no electron density was seen for ...SEQUENCE Authors also crystallized the sequence CGATGCTA, however no electron density was seen for any of the residues. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rxv.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rxv.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 1rxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rxv_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 1rxv_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 1rxv_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 1rxv_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxv ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Each monomer of the dimer in the asymmetric unit represents one complete biological assembly unit. |
-Components
#1: DNA chain | Mass: 2755.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic upstream primer DNA #2: Protein | Mass: 38117.398 Da / Num. of mol.: 2 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 |
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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: 2.88 Å3/Da / Density % sol: 57.29 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: MPEG 5000, sodium acetate, ethylene glycol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 21 ℃ / 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: 2.5→40 Å / Num. all: 33196 / Num. obs: 33196 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.054 |
Reflection shell | Resolution: 2.5→2.59 Å / Rsym value: 0.192 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model built from 2.5A resolution experimental map. Phases for this map were calculated from a four-wavelength multiple anomalous dispersion experiment. Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.238 / Rfactor Rwork: 0.242 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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