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- PDB-1pjj: Complex between the Lactococcus lactis Fpg and an abasic site con... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pjj | ||||||
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Title | Complex between the Lactococcus lactis Fpg and an abasic site containing DNA. | ||||||
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![]() | hydrolase/DNA / DNA repair / Fpg / MutM / abasic site / 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: 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 th 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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Remark 999 | sequence The author maintains that the Asp137 is an error in the sequence database. This residue ...sequence The author maintains that the Asp137 is an error in the sequence database. This residue does not exist. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.8 KB | Display | ![]() |
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PDB format | ![]() | 66.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.5 KB | Display | ![]() |
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Full document | ![]() | 472.6 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nnjC ![]() 1pjiC ![]() 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
-DNA chain , 2 types, 2 molecules DE
#1: DNA chain | Mass: 4054.614 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 OR FPG / Plasmid: pmal-c / Production host: ![]() ![]() References: UniProt: P42371, DNA-formamidopyrimidine glycosylase |
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-Non-polymers , 3 types, 282 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 | ChemComp-ZN / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.43 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: citrate, Hepes, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
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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: 1.9→43.7 Å / Num. all: 48837 / Num. obs: 48787 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 27.689 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.073 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 0.8 / Num. unique all: 7019 / Rsym value: 0.488 / % possible all: 100 |
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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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