+Open data
-Basic information
Entry | Database: PDB / ID: 2izo | ||||||
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Title | Structure of an Archaeal PCNA1-PCNA2-FEN1 Complex | ||||||
Components |
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Keywords | HYDROLASE / DNA REPAIR / DNA-BINDING / ENDONUCLEASE / METAL-BINDING / EXCISION REPAIR / DNA REPLICATION / PCNA / FEN1 / NUCLEASE / MAGNESIUM | ||||||
Function / homology | Function and homology information flap endonuclease activity / 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 / DNA replication ...flap endonuclease activity / 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 / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Dore, A.S. / Kilkenny, M.L. / Roe, S.M. / Pearl, L.H. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2006 Title: Structure of an Archaeal PCNA1-PCNA2-Fen1 Complex: Elucidating PCNA Subunit and Client Enzyme Specificity. Authors: Dore, A.S. / Kilkenny, M.L. / Jones, S.A. / Oliver, A.W. / Roe, S.M. / Bell, S.D. / Pearl, L.H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2izo.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2izo.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 2izo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2izo_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 2izo_full_validation.pdf.gz | 465 KB | Display | |
Data in XML | 2izo_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 2izo_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/2izo ftp://data.pdbj.org/pub/pdb/validation_reports/iz/2izo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39358.312 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET33B / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q980U8, Hydrolases; Acting on ester bonds |
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-DNA POLYMERASE SLIDING CLAMP ... , 2 types, 2 molecules BC
#2: Protein | Mass: 27551.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97Z84 |
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#3: Protein | Mass: 27569.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P57766 |
-Non-polymers , 3 types, 86 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CHAIN A: ENDONUCLEASE THAT CLEAVES THE 5' OVERHANGING FLAP STRUCTURE THAT IS GENERATED BY ...CHAIN A: ENDONUCLEA |
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Sequence details | FIRST FOUR RESIDUES REMOVED FOR CONSTRUCT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 50 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: PRIOR TO CRYSTALLISATION THE PCNA1-PCNA2-PCNA3 COMPLEX WAS MIXED WITH FEN1 AT AN EQUIMOLAR RATIO AND INCUBATED FOR 20 MIN AT 294 K. PCNA1-PCNA2-FEN1 CO-CRYSTALS WERE GROWN BY THE VAPOUR ...Details: PRIOR TO CRYSTALLISATION THE PCNA1-PCNA2-PCNA3 COMPLEX WAS MIXED WITH FEN1 AT AN EQUIMOLAR RATIO AND INCUBATED FOR 20 MIN AT 294 K. PCNA1-PCNA2-FEN1 CO-CRYSTALS WERE GROWN BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS. PCNA3 WAS NOT PRESENT IN THE CRYSTAL LATTICE. DROPS WERE PREPARED BY MIXING 100 MM PROTEIN COMPLEX IN 20 MM TRIS-HCL PH 8.0, 200 MM NACL, 5 MM MGCL2, 2 MM DTT BUFFER SOLUTION WITH EQUAL VOLUMES OF 0.1M ACETATE PH 4.8, 8% PEG 8,000, 220 MM ZNOAC2 AND 30 MM GLYCYL-GLYCYL-GLYCINE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60 Å / Num. obs: 23534 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 71.32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1B43 FOR FEN1 AND 1VYJ FOR PCNA1 AND PCNA2 Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.848 / SU B: 40.663 / SU ML: 0.388 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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