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Open data
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Basic information
Entry | Database: PDB / ID: 7ui4 | ||||||
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Title | Crystal structure of the DNA preQ0 insertase DpdA | ||||||
![]() | DNA-guanine transglycosylase | ||||||
![]() | DNA BINDING PROTEIN / 2'-deoxy-7-cyano-7-deazaguanosine / dPreQ0 / DNA modification / DNA-guanine transglycosylase | ||||||
Function / homology | pentosyltransferase activity / tRNA modification / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / tRNA-guanine transglycosylase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hung, S.-H. / Swairjo, M.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Authors: Gedara, S.H. / Wood, E. / Gustafson, A. / Liang, C. / Hung, S.H. / Savage, J. / Phan, P. / Luthra, A. / de Crecy-Lagard, V. / Dedon, P. / Swairjo, M.A. / Iwata-Reuyl, 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 | ![]() | 189.5 KB | Display | ![]() |
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PDB format | ![]() | 149.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 919 KB | Display | ![]() |
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Full document | ![]() | 922.4 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50344.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: AIG37_01840, APO85_00905, AU259_04380, AVH73_05845, AVH73_21940, AXU14_04585, AXU32_02035, B0D32_05855, B0D32_22885, B5881_18565, B6C67_03300, B6C67_22040, BIW02_04385, BIW02_22200, C2689_ ...Gene: AIG37_01840, APO85_00905, AU259_04380, AVH73_05845, AVH73_21940, AXU14_04585, AXU32_02035, B0D32_05855, B0D32_22885, B5881_18565, B6C67_03300, B6C67_22040, BIW02_04385, BIW02_22200, C2689_01835, C2689_23730, CW117_05915, D0215_03875, D0215_23815, D2K49_10730, DK664_02155, DK664_23285, DPL19_04880, DPL19_23835, DQS63_22335, DT992_19130, DT992_25255, DYO72_07125, DYO72_24190, DYT96_02055, E0U36_08570, E0U36_22475, E4933_05800, E4S88_01055, E4S88_22855, EIC46_05430, FEH78_03570, G2910_01835, G2910_23335, G2911_06635, G2911_23200, G3401_000792, G4B33_001303, G4Y15_003124, G4Y21_000316, G4Y22_001365, G9254_000030, G9254_004691, G9G43_001321, G9G43_004619, II32_05770 Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: mixing 2 ul sample containing 4.0 mg/ml protein (81.5 uM), 0.5 mM guanine, 50 mM Tris (pH 7.5), 100 mM NaCl and 1 mM DTT with 3 ul reservoir solution containing 10% (w/v) polyethylene glycol ...Details: mixing 2 ul sample containing 4.0 mg/ml protein (81.5 uM), 0.5 mM guanine, 50 mM Tris (pH 7.5), 100 mM NaCl and 1 mM DTT with 3 ul reservoir solution containing 10% (w/v) polyethylene glycol (PEG) 8000, 8% (v/v) ethylene glycol (EG), 100 mM HEPES (pH 7.5), 0.1 mM ZnCl2, 3 mM reduced glutathione (GSH) and 3 mM oxidized glutathione (GSSG) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.51→73.59 Å / Num. obs: 16179 / % possible obs: 87.1 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Rrim(I) all: 0.107 / Net I/σ(I): 21.8 / Num. measured all: 207845 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.18 Å2 / Biso mean: 55.874 Å2 / Biso min: 34.52 Å2
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Refinement step | Cycle: final / Resolution: 2.51→54.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.574 Å / Rfactor Rfree error: 0
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