+Open data
-Basic information
Entry | Database: PDB / ID: 3nm5 | ||||||
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Title | Helicobacter pylori MTAN complexed with Formycin A | ||||||
Components | MTA/SAH nucleosidase | ||||||
Keywords | HYDROLASE / nucleosidase | ||||||
Function / homology | Function and homology information aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Ronning, D.R. / Iacopelli, N.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Enzyme-ligand interactions that drive active site rearrangements in the Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. Authors: Ronning, D.R. / Iacopelli, N.M. / Mishra, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nm5.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nm5.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 3nm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/3nm5 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/3nm5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25049.900 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: jhp_0082, mtn, mtnN, Pfs / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9ZMY2, adenosylhomocysteine nucleosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 16 % w/v PEG 8000, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 47622 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Redundancy: 5 % / Rsym value: 0.061 / Net I/σ(I): 10 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→39.098 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / 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: 59.792 Å2 / ksol: 0.427 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→39.098 Å
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Refine LS restraints |
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LS refinement shell |
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