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Yorodumi- PDB-4pcz: Crystal structure of a complex between R247G LlFPG mutant and a T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pcz | ||||||
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Title | Crystal structure of a complex between R247G LlFPG mutant and a THF containing DNA | ||||||
Components |
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Keywords | Hydrolase/DNA / DNA glycosylase / THF / Hydrolase-DNA complex | ||||||
Function / homology | Function and homology information 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 | Lactococcus lactis subsp. cremoris (lactic acid bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Coste, F. / Castaing, B. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization. Authors: Biela, A. / Coste, F. / Culard, F. / Guerin, M. / Goffinont, S. / Gasteiger, K. / Ciesla, J. / Winczura, A. / Kazimierczuk, Z. / Gasparutto, D. / Carell, T. / Tudek, B. / Castaing, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pcz.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pcz.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pcz_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 4pcz_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 4pcz_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4pcz_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/4pcz ftp://data.pdbj.org/pub/pdb/validation_reports/pc/4pcz | HTTPS FTP |
-Related structure data
Related structure data | 4pd2C 4pdgC 4pdiC 1pm5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31016.072 Da / Num. of mol.: 1 / Mutation: R247G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Gene: mutM, fpg / Production host: Escherichia coli (E. coli) References: UniProt: P42371, DNA-formamidopyrimidine glycosylase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4054.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 455 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.94 Å / Num. obs: 65739 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.6 / % possible all: 88.2 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PM5 Resolution: 1.7→47.94 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 18.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→47.94 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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