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Open data
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Basic information
Entry | Database: PDB / ID: 3spd | ||||||
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Title | Crystal structure of aprataxin ortholog Hnt3 in complex with DNA | ||||||
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![]() | HYDROLASE/DNA / HIT domain / Zinc Finger / DNA deadenylase / DNA Binding / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() guanosine binding / adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / GMP binding / single-strand break-containing DNA binding / single strand break repair / mismatched DNA binding / mismatch repair ...guanosine binding / adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / GMP binding / single-strand break-containing DNA binding / single strand break repair / mismatched DNA binding / mismatch repair / double-stranded RNA binding / single-stranded DNA binding / double-stranded DNA binding / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gong, Y. / Zhu, D. / Ding, J. / Dou, C. / Ren, X. / Jiang, T. / Wang, D. | ||||||
![]() | ![]() Title: Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA Authors: Gong, Y. / Zhu, D. / Ding, J. / Dou, C. / Ren, X. / Gu, L. / Jiang, T. / Wang, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.1 KB | Display | ![]() |
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PDB format | ![]() | 182 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.7 KB | Display | ![]() |
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Full document | ![]() | 496.7 KB | Display | |
Data in XML | ![]() | 44.1 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sp4SC ![]() 3splC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23608.061 Da / Num. of mol.: 4 / Fragment: UNP residues 33-232 / Mutation: C130A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 38366 / 972 / Gene: hnt3, SPCC18.09c / Plasmid: pET28a / Production host: ![]() ![]() |
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-DNA chain , 2 types, 4 molecules EGFH
#2: DNA chain | Mass: 4583.996 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DNA oligonucleotides were synthesized from Shanghai Sangon Biotechnology Company (Shanghai, China). #3: DNA chain | Mass: 5251.423 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DNA oligonucleotides were synthesized from Shanghai Sangon Biotechnology Company (Shanghai, China) |
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-Non-polymers , 3 types, 1125 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6M Ammonium Sulfate, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2010 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. all: 96371 / Num. obs: 96371 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9158 / Rsym value: 0.481 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SP4 Resolution: 1.912→23.496 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 1.69 / σ(F): 0.12 / σ(I): 0.12 / Phase error: 20.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.38 Å2 / ksol: 0.375 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.45 Å2 / Biso mean: 27.2893 Å2 / Biso min: 11.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.912→23.496 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: 30
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