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Yorodumi- PDB-1ee8: CRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ee8 | ||||||
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Title | CRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8 | ||||||
Components | MUTM (FPG) PROTEIN | ||||||
Keywords | DNA BINDING PROTEIN / BETA SANDWICH / ZINC FINGER / HELIX TWO-TURNS HELIX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion 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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Sugahara, M. / Mikawa, T. / Kumasaka, T. / Yamamoto, M. / Kato, R. / Fukuyama, K. / Inoue, Y. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8. Authors: Sugahara, M. / Mikawa, T. / Kumasaka, T. / Yamamoto, M. / Kato, R. / Fukuyama, K. / Inoue, Y. / Kuramitsu, S. #1: Journal: Nucleic Acids Res. / Year: 1998 Title: Termostable Repair Enzyme for Oxidative DNA Damage from Extremely Thermophilic Bacterium, Thermus Thermophilus HB8 Authors: Mikawa, T. / Kato, R. / Sugahara, M. / Kuramitsu, S. #2: Journal: J.BIOCHEM.(TOKYO) / Year: 2000 Title: Crystallization and Preliminary X-ray Crystallographic Studies of Thermus Thermophilus HB8 MutM Protein Involved in Repairs Oxidative DNA Damage Authors: Sugahara, M. / Mikawa, T. / Kato, R. / Kumasaka, T. / Yamamoto, M. / Fukuyama, K. / Inoue, Y. / kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ee8.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ee8.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ee8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ee8_validation.pdf.gz | 369.8 KB | Display | wwPDB validaton report |
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Full document | 1ee8_full_validation.pdf.gz | 379.3 KB | Display | |
Data in XML | 1ee8_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 1ee8_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1ee8 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1ee8 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29833.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50606 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.8 Details: PEG MME 2000, 2-mercaptoethanol, CHES, pH 9.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal grow | *PLUS Details: Sugahara, M., (2000) J. Biochem., 127, 9. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 37892 / Num. obs: 37892 / % possible obs: 0.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 25.65 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.96 % / Rmerge(I) obs: 0.91 / Num. unique all: 1730 / % possible all: 0.821 |
Reflection | *PLUS % possible obs: 90 % / Num. measured all: 402397 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 82.1 % / Num. unique obs: 1729 / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2 |
-Processing
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Refinement | Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.214 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.82 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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