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Yorodumi- PDB-1pm5: Crystal structure of wild type Lactococcus lactis Fpg complexed t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pm5 | ||||||
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Title | Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran containing DNA | ||||||
Components |
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Keywords | hydrolase/DNA / DNA repair / Fpg / MutM / abasic site / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Pereira de Jesus-Tran, K. / Serre, L. / Zelwer, C. / Castaing, B. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2005 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: Journal: Embo J. / Year: 2002 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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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pm5.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pm5.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pm5_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 1pm5_full_validation.pdf.gz | 468.6 KB | Display | |
Data in XML | 1pm5_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1pm5_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/1pm5 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/1pm5 | HTTPS FTP |
-Related structure data
Related structure data | 1nnjSC 1pjiC 1pjjC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | the biological assembly corresponds to one Fpg molecule and one DNA duplex |
-Components
-DNA chain , 2 types, 2 molecules DE
#1: DNA chain | Mass: 4054.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synyhetic |
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#2: DNA chain | Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 31116.217 Da / Num. of mol.: 1 / Fragment: Fpg Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Species: Lactococcus lactis / Strain: subsp. cremoris / Gene: MUTM OR FPG / Plasmid: PMAL-C / Production host: Escherichia coli (E. coli) References: UniProt: P42371, DNA-formamidopyrimidine glycosylase |
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-Non-polymers , 3 types, 310 molecules
#4: Chemical | ChemComp-ZN / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.18 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: citrate, hepes, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 14, 2003 |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→77 Å / Num. all: 43785 / Num. obs: 43717 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 29.042 Å2 / Rsym value: 0.045 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4 / Rsym value: 0.147 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NNJ Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.9 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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LS refinement shell | Resolution: 1.95→1.97 Å /
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