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- PDB-1nnj: Crystal structure Complex between the Lactococcus lactis Fpg and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nnj | ||||||
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Title | Crystal structure Complex between the Lactococcus lactis Fpg and an abasic site containing DNA | ||||||
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![]() | HYDROLASE / DNA repair / Fpg / MutM / abasic site | ||||||
Function / homology | ![]() DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Serre, L. / Pereira de Jesus, K. / Boiteux, S. / Zelwer, C. / Castaing, B. | ||||||
![]() | ![]() Title: Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA. Authors: Pereira de Jesus, K. / Serre, L. / Zelwer, C. / Castaing, B. #1: ![]() Title: Crystallization and primary X-ray crystallographic studies of a complex between the Lactococcus lactis Fpg DNA-repair enzyme and an abasic site containing DNA Authors: Pereira de Jesus, K. / Serre, L. / Hervouet, N. / Bouckson-Castaing, V. / Zelwer, C. / Castaing, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.9 KB | Display | ![]() |
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PDB format | ![]() | 64.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pjiC ![]() 1pjjC ![]() 1pm5C ![]() 1kfvS S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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Components
-DNA chain , 2 types, 2 molecules DE
#1: DNA chain | Mass: 4012.577 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 31076.154 Da / Num. of mol.: 1 / Mutation: P1G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MUTM / Plasmid: pmal-c / Production host: ![]() ![]() References: UniProt: P42371, DNA-formamidopyrimidine glycosylase |
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-Non-polymers , 3 types, 230 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 65.9 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: citrate, Hepes, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2002 |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44 Å / Num. all: 56976 / Num. obs: 56858 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.074 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.2 / Num. unique all: 7923 / Rsym value: 0.627 / % possible all: 94.8 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 44 Å / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS Rmerge(I) obs: 0.627 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KFV Resolution: 1.9→35 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→35 Å
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LS refinement shell | Resolution: 1.9→1.91 Å /
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Refinement | *PLUS Lowest resolution: 35 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Rfactor Rfree: 0.29 |