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Yorodumi- PDB-1q3b: Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q3b | ||||||
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Title | Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The R252A mutant at 2.05 resolution. | ||||||
Components | Endonuclease VIII | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA-(apurinic or apyrimidinic site) endonuclease 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Golan, G. / Zharkov, D.O. / Feinberg, H. / Fernandes, A.S. / Zaika, E.I. / Kycia, J.H. / Grollman, A.P. / Shoham, G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2005 Title: Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. Authors: Golan, G. / Zharkov, D.O. / Feinberg, H. / Fernandes, A.S. / Zaika, E.I. / Kycia, J.H. / Grollman, A.P. / Shoham, G. | ||||||
History |
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Remark 999 | SEQUENCE SEQUENCING AND CRYSTALLOGRAPHY CONFIRM THE SEQUENCE AS THR A 34 AND ARG A 112. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q3b.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q3b.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q3b_validation.pdf.gz | 379.2 KB | Display | wwPDB validaton report |
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Full document | 1q3b_full_validation.pdf.gz | 384 KB | Display | |
Data in XML | 1q3b_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1q3b_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/1q3b ftp://data.pdbj.org/pub/pdb/validation_reports/q3/1q3b | HTTPS FTP |
-Related structure data
Related structure data | 1q39C 1q3cC 1k3wS 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
#1: Protein | Mass: 29728.877 Da / Num. of mol.: 1 / Mutation: R252A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NEI / Plasmid: PET13A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: P50465, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 3.29 Å3/Da / Density % sol: 62.59 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 35% PEG 400, 0.1M Tris-HCl pH 8.4, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.102 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 22, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.102 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. all: 25032 / Num. obs: 25032 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.43 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 5 % / Rmerge(I) obs: 0.421 / Num. unique all: 1220 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The Protein chain from PDB code 1K3W Resolution: 2.05→29.21 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.3061 Å2 / ksol: 0.357914 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→29.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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