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- PDB-5kb3: 1.4 A resolution structure of Helicobacter Pylori MTAN in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kb3 | |||||||||
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Title | 1.4 A resolution structure of Helicobacter Pylori MTAN in complexed with p-ClPh-DADMe-ImmA | |||||||||
![]() | Aminodeoxyfutalosine nucleosidase | |||||||||
![]() | HYDROLASE / nucleosidase / helicobacter pylori / neutron crystallography | |||||||||
Function / homology | ![]() aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / nucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Banco, M.T. / Ronning, D.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states. Authors: Banco, M.T. / Mishra, V. / Ostermann, A. / Schrader, T.E. / Evans, G.B. / Kovalevsky, A. / Ronning, D.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.9 KB | Display | ![]() |
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PDB format | ![]() | 81.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 737.7 KB | Display | ![]() |
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Full document | ![]() | 738.8 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ccdC ![]() 5cceC ![]() 5jpcC ![]() 5k1zC ![]() 3nm5S C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 24975.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: J99 / ATCC 700824 / Gene: mtnN, mtn, jhp_0082 / Production host: ![]() ![]() References: UniProt: Q9ZMY2, aminodeoxyfutalosine nucleosidase, adenosylhomocysteine nucleosidase |
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#2: Chemical | ChemComp-4CT / ( |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 100 mM HEPES pH 7.5, 18 % w/v polyethylene glycol 550 monomethyl ether, and 95 mM magnesium chloride hexahydrate. |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.399→34.76 Å / Num. obs: 50579 / % possible obs: 99.3 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.445 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NM5 Resolution: 1.399→34.76 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.51 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.399→34.76 Å
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Refine LS restraints |
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LS refinement shell |
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