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- PDB-1kfv: Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kfv | ||||||
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Title | Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA. | ||||||
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![]() | HYDROLASE/DNA / DNA repair enzyme / Abasic site / DNA / N-glycosylase / AP lyase / HYDROLASE-DNA COMPLEX | ||||||
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: Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA. Authors: Serre, L. / Pereira de Jesus, K. / Boiteux, S. / 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 | ![]() | 148.4 KB | Display | ![]() |
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PDB format | ![]() | 112.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ee8S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 4 molecules DGEH
#1: DNA chain | Mass: 3683.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: contains a 1,3 propanediol site (PDI) #2: DNA chain | Mass: 4066.702 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 31263.736 Da / Num. of mol.: 2 / Mutation: P1G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MUTM or FPG / Plasmid: pMAL-c / Production host: ![]() ![]() References: UniProt: P42371, DNA-formamidopyrimidine glycosylase |
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-Non-polymers , 3 types, 58 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.05 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: PEG4K, LiSO4, TCEP, Tris-HCl, spermidine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.6 / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Jun 20, 2001 / Details: mirrors |
Radiation | Monochromator: Si (111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→25 Å / Num. all: 22185 / Num. obs: 21897 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.053 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.54→2.67 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.209 / % possible all: 94.3 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS Rmerge(I) obs: 0.288 |
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Processing
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Refinement | Method to determine structure: Molecular replacement combined with MAD Starting model: PDB ENTRY 1EE8 Resolution: 2.55→25 Å / Isotropic thermal model: overall / Cross valid method: free R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: NCS restraints have been considered during refinement. THERE ARE TWO POSSIBLE POSITIONS FOR THE ZN ATOM IN MOLECULE B (SEE AZN and BZN).
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Displacement parameters | Biso mean: 40 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.57 Å / Total num. of bins used: 43
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.251 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.4 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.38 / Rfactor Rwork: 0.35 |