double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA binding / metal ion binding Similarity search - Function
AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.01 Å3/Da / Density % sol: 38.5 %
Crystal grow
Method: vapor diffusion, hanging drop / pH: 9 Details: 24 WELL LINBRO PLATES USED FOR HANGING DROP EXPERIMENTS WITH 0.5 UL PROTEIN AND 0.5 UL WELL SOLUTION FOR THE DROPS. PROTEIN CONCENTRATION 20 MG/ML, IN 10 MM TRIS, PH 7.0 AND 100 MM NACL. THE ...Details: 24 WELL LINBRO PLATES USED FOR HANGING DROP EXPERIMENTS WITH 0.5 UL PROTEIN AND 0.5 UL WELL SOLUTION FOR THE DROPS. PROTEIN CONCENTRATION 20 MG/ML, IN 10 MM TRIS, PH 7.0 AND 100 MM NACL. THE WELL SOLUTION CONTAINED 20% PEG 20000, 0.1 M BICINE PH 9.0, 2% DIOXANE.
Resolution: 1.5→29.53 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.298 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES HAVE ATOMS MISSING FROM THE SIDECHAINS BECAUSE THERE WAS NO DENSITY FOR THESE ATOMS IN THE ELECTRON DENSITY MAPS ARG ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES HAVE ATOMS MISSING FROM THE SIDECHAINS BECAUSE THERE WAS NO DENSITY FOR THESE ATOMS IN THE ELECTRON DENSITY MAPS ARG 64, ARG 75, GLU 87, GLU 177, LYS 181, LYS 185, AND GLU 259.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.159
1774
5 %
RANDOM
Rwork
0.12
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obs
0.123
35412
100 %
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Solvent computation
Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK