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Yorodumi- PDB-1rxz: C-terminal region of A. fulgidus FEN-1 complexed with A. fulgidus PCNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rxz | ||||||
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Title | C-terminal region of A. fulgidus FEN-1 complexed with A. fulgidus PCNA | ||||||
Components |
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Keywords | REPLICATION / beta-zipper / interdomain connecting loop / DNA repair / DNA replication | ||||||
Function / homology | Function and homology information 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / RNA-DNA hybrid ribonuclease activity / manganese ion binding ...5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / 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 | 1rxz.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rxz.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rxz_validation.pdf.gz | 428.8 KB | Display | wwPDB validaton report |
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Full document | 1rxz_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 1rxz_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1rxz_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxz ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxz | HTTPS FTP |
-Related structure data
Related structure data | 1rwzSC 1rxmC 1rxvC 1rxwC 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 trimer generated from the monomer in the asymmetric unit by applying the following transformations: ROTATION: [-0.5 -0.86603 0] [0.86603 -0.5 0] [0 0 1] TRANSLATION: 86.53304 -0.00002 0.00002 AND ROTATION: [-0.5 0.86603 0] [-0.86603 -0.5 0] [0 0 1] TRANSLATION: 43.26651 74.9398 0.00003 |
-Components
#1: Protein | Mass: 27301.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: PCN, AF0335 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29912 |
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#2: Protein/peptide | Mass: 1368.536 Da / Num. of mol.: 1 / Fragment: PCNA-binding motif / Source method: obtained synthetically Details: synthetic peptide derived from the PCNA-binding motif of afFEN-1 References: UniProt: O29975 |
#3: 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: 2.43 Å3/Da / Density % sol: 49.39 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Na/K phosphate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2003 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 2→60 Å / Num. all: 36466 / Num. obs: 36466 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.08 |
Reflection shell | Resolution: 2→2.1 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.457 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RWZ Resolution: 2→60 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Carried out twinned refinement in CNS, against the least squares residual for hemihedral twinning. The twinning operator is: h,-h-k,-l. The twin fraction is: 0.370
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Refinement step | Cycle: LAST / Resolution: 2→60 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.26 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |