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Yorodumi- PDB-3zda: Structure of E. coli ExoIX in complex with a fragment of the Flap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zda | ||||||
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Title | Structure of E. coli ExoIX in complex with a fragment of the Flap1 DNA oligonucleotide, potassium and magnesium | ||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / FLAP ENDONUCLEASE / DNA BINDING | ||||||
Function / homology | Function and homology information DNA replication, Okazaki fragment processing / 5'-flap endonuclease activity / 5'-3' exonuclease activity / potassium ion binding / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Hemsworth, G.R. / Anstey-Gilbert, C.S. / Flemming, C.S. / Hodskinson, M.R.G. / Zhang, J. / Sedelnikova, S.E. / Stillman, T.J. / Sayers, J.R. / Artymiuk, P.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases Authors: Anstey-Gilbert, C.S. / Hemsworth, G.R. / Flemming, C.S. / Hodskinson, M.R.G. / Zhang, J. / Sedelnikova, S.E. / Stillman, T.J. / Sayers, J.R. / Artymiuk, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zda.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zda.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zda_validation.pdf.gz | 464.3 KB | Display | wwPDB validaton report |
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Full document | 3zda_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 3zda_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3zda_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/3zda ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zda | HTTPS FTP |
-Related structure data
Related structure data | 3zd8C 3zd9SC 3zdbC 3zdcC 3zddC 3zdeC C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28203.158 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: XL-1 BLUE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PCI857 References: UniProt: Q8X6R9, Hydrolases; Acting on ester bonds |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: DNA chain | Mass: 1818.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 5 types, 247 molecules
#4: Chemical | ChemComp-K / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-PIV / |
#7: Chemical | ChemComp-PO4 / |
#8: Water | ChemComp-HOH / |
-Details
Sequence details | FRAGMENT OF LARGER DNA BOUND TO PROTEIN. SEQUENCE IS ACTUALLY UNKNOWN, CRYSTAL LIKELY HAS MIXED ...FRAGMENT OF LARGER DNA BOUND TO PROTEIN. SEQUENCE IS ACTUALLY UNKNOWN, CRYSTAL LIKELY HAS MIXED DNAS BOUND HERE. |
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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.2 M MAGNESIUM ACETATE, 15% (W/V) PEG-3350, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 16, 2008 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→51.64 Å / Num. obs: 57905 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZD9 Resolution: 1.5→51.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.333 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / 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: 25.205 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→51.64 Å
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Refine LS restraints |
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