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- PDB-3zdd: Structure of E. coli ExoIX in complex with the palindromic 5ov6 o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zdd | ||||||
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Title | Structure of E. coli ExoIX in complex with the palindromic 5ov6 oligonucleotide and potassium | ||||||
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![]() | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / ENDONUCLEASE / DNA BINDING | ||||||
Function / homology | ![]() 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Flemming, C.S. / Hemsworth, G.R. / Anstey-Gilbert, C.S. / Hodskinson, M.R.G. / Zhang, J. / Sedelnikova, S.E. / Stillman, T.J. / Sayers, J.R. / Artymiuk, P.J. | ||||||
![]() | ![]() Title: The structure of Escherichia 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. / 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 | ![]() | 77.4 KB | Display | ![]() |
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PDB format | ![]() | 54.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zd8C ![]() 3zd9C ![]() 3zdaC ![]() 3zdbC ![]() 3zdcC ![]() 3zdeC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein / DNA chain , 2 types, 2 molecules AB
#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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#2: DNA chain | Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 223 molecules ![](data/chem/img/K.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-K / |
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#4: Chemical | ChemComp-IPA / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | OLIGO DESIGNED BASED ON INITIAL STRUCTURE WITH FRAGMENT OF LARGER DNA.THE GENBACK REFERENCE ...OLIGO DESIGNED BASED ON INITIAL STRUCTURE WITH FRAGMENT OF LARGER DNA.THE GENBACK REFERENCE PROVIDED BY AUTHOR FOR CHAIN A IS ZP_02776037.1 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M HEPES PH 7.5, 10 % ISOPROPANOL, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→31.15 Å / Num. obs: 54849 / % possible obs: 98.1 % / Observed criterion σ(I): 6 / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: EXOIX FLAP1 FRAGMENT COMPLEX STRUCTURE Resolution: 1.5→30.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.694 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.588 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.34 Å
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Refine LS restraints |
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