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Yorodumi- PDB-1orp: Structure of a Trapped Endonuclease III-DNA Covalent Intermediate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1orp | ||||||
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Title | Structure of a Trapped Endonuclease III-DNA Covalent Intermediate: Estranged-Adenine 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 / FOURIER SYNTHESIS / Resolution: 2.2 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 sequence of the protein has not yet been published. Residues Gly -2, Ser - ...Authors informed that the sequence of the protein 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 | 1orp.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1orp.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 1orp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1orp ftp://data.pdbj.org/pub/pdb/validation_reports/or/1orp | HTTPS FTP |
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-Related structure data
Related structure data | 1ornSC 1p59C 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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-Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3391.250 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 , 3 types, 73 molecules
#4: Chemical | ChemComp-NA / |
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#5: Chemical | ChemComp-SF4 / |
#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: 2.59 Å3/Da / Density % sol: 52.07 % | ||||||||||||||||||||||||||||||
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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: 2.2→30 Å / Num. all: 16279 / Num. obs: 15614 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1689 / % possible all: 99.2 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 99.2 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1ORN Resolution: 2.2→24.51 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 570754.36 / Data cutoff high rms absF: 570754.36 / 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: 74.6102 Å2 / ksol: 0.390554 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→24.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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