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- PDB-3zda: Structure of E. coli ExoIX in complex with a fragment of the Flap... -
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Open data
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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 | ||||||
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![]() | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / FLAP ENDONUCLEASE / DNA BINDING | ||||||
Function / homology | ![]() DNA replication, Okazaki fragment processing / 5'-flap endonuclease activity / potassium ion binding / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.8 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.3 KB | Display | ![]() |
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Full document | ![]() | 466.5 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zd8C ![]() 3zd9SC ![]() 3zdbC ![]() 3zdcC ![]() 3zddC ![]() 3zdeC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() 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 ![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PIV.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PIV.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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