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Yorodumi- PDB-1orn: Structure of a Trapped Endonuclease III-DNA Covalent Intermediate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1orn | ||||||
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Title | Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Guanine Complex | ||||||
Components |
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Keywords | HYDROLASE/DNA / DNA repair / DNA glycosylase / [4Fe-4S] cluster / iron-sulfur cluster / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha / IRON/SULFUR CLUSTER / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å | ||||||
Authors | Fromme, J.C. / Verdine, G.L. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structure of a Trapped Endonuclease III-DNA Covalent Intermediate Authors: Fromme, J.C. / Verdine, G.L. | ||||||
History |
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Remark 999 | Authors informed that the protein sequence has not yet been published. Residues Gly -2, Ser -1 and ...Authors informed that the protein sequence has not yet been published. Residues Gly -2, Ser -1 and His 0 are cloning artifacts. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1orn.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1orn.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1orn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1orn ftp://data.pdbj.org/pub/pdb/validation_reports/or/1orn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3407.249 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3193.089 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 26234.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: nth / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(C41) |
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-Non-polymers , 4 types, 108 molecules
#4: Chemical | ChemComp-TRS / |
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#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-SF4 / |
#7: 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: 2.46 Å3/Da / Density % sol: 49.51 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, Tris, beta-mercaptoethanol , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9363 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 19, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9363 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 33952 / Num. obs: 33490 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3 / Num. unique all: 3328 / % possible all: 99.6 |
Reflection shell | *PLUS % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.7→29.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1581342.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.323 Å2 / ksol: 0.40271 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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