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- PDB-4ojt: Helicobacter pylori MTAN complexed with S-ribosylhomocysteine and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ojt | |||||||||
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Title | Helicobacter pylori MTAN complexed with S-ribosylhomocysteine and adenine | |||||||||
![]() | MTA/SAH nucleosidase | |||||||||
![]() | HYDROLASE / Homodimer | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Mishra, V. / Ronning, D.R. | |||||||||
![]() | ![]() Title: Crystal structures of the Helicobacter pylori MTAN enzyme reveal specific interactions between S-adenosylhomocysteine and the 5'-alkylthio binding subsite. Authors: Mishra, V. / 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 | ![]() | 62.2 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.4 KB | Display | ![]() |
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Full document | ![]() | 726.4 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 25106.951 Da / Num. of mol.: 1 / Fragment: UNP residues 2-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9ZMY2, adenosylhomocysteine nucleosidase |
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#2: Sugar | ChemComp-2WP / |
#3: Chemical | ChemComp-ADE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05 M magnesium chloride hexahydrate, 0.1 M HEPES, 30 % (v/v) PEG-MME 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2011 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 40628 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 46.389 |
Reflection shell | Resolution: 1.5→1.5402 Å / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.346 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→34.798 Å
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Refine LS restraints |
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LS refinement shell |
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