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Open data
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Basic information
Entry | Database: PDB / ID: 3ga6 | ||||||
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Title | Mth0212 in complex with two DNA helices | ||||||
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![]() | HYDROLASE/DNA / protein-DNA complex / twin / disorder of DNA / 3'-5' exonuclease / AP endonuclease / 2'-desoxyuridine endonuclease / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / endonuclease activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lakomek, K. / Dickmanns, A. / Ficner, R. | ||||||
![]() | ![]() Title: Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA Authors: Lakomek, K. / Dickmanns, A. / Ciirdaeva, E. / Schomacher, L. / Ficner, R. #1: Journal: Nucleic Acids Res. / Year: 2006 Title: The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease Authors: Georg, J. / Schomacher, L. / Chong, J.P.J. / Majernik, A.I. / Raabe, M. / Urlaub, H. / Muller, S. / Ciirdaeva, E. / Kramer, W. / Fritz, H.-J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.8 KB | Display | ![]() |
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PDB format | ![]() | 205.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.3 KB | Display | ![]() |
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Full document | ![]() | 519.3 KB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fziSC ![]() 3g00C ![]() 3g0aC ![]() 3g0rC ![]() 3g1kC ![]() 3g2cC ![]() 3g2dC ![]() 3g38C ![]() 3g3cC ![]() 3g3yC ![]() 3g4tC ![]() 3g8vC ![]() 3g91C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31429.666 Da / Num. of mol.: 2 / Mutation: T1002/2002A, D1151/2151N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Delta H (DSM 1053) / Gene: mth0212, MTH212, MTH_212 / Plasmid: pET_B_001-mth212 (D151N) / Production host: ![]() ![]() |
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-DNA chain , 2 types, 4 molecules FHGD
#2: DNA chain | Mass: 3704.404 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 3625.341 Da / Num. of mol.: 2 / Source method: obtained synthetically |
-Non-polymers , 4 types, 376 molecules 






#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-NA / |
#6: Chemical | |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.84 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: reservoir solution: 5% (w/v) PEG 8000, 200mM KCl, 10 mM MgCl2, 50mM MES pH 5.6, 2mM DTT; complex solution: 245mM NaCl, 8mM HEPES-KOH pH 7.6, 2mM MgCl2, 3mM DTT , VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection twin | Operator: l,-k,h / Fraction: 0.505 |
Reflection | Resolution: 1.898→50 Å / Num. obs: 56272 / % possible obs: 95.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.075 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.898→1.97 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.607 / % possible all: 72.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3FZI Resolution: 1.898→33.709 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.851 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.625 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 223.5 Å2 / Biso mean: 36.76 Å2 / Biso min: 11.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.898→33.709 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %
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Refinement TLS params. | S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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