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Yorodumi- PDB-4ojt: Helicobacter pylori MTAN complexed with S-ribosylhomocysteine and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ojt | |||||||||
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Title | Helicobacter pylori MTAN complexed with S-ribosylhomocysteine and adenine | |||||||||
Components | MTA/SAH nucleosidase | |||||||||
Keywords | HYDROLASE / Homodimer | |||||||||
Function / homology | Function and homology information aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | Helicobacter pylori (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Mishra, V. / Ronning, D.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ojt.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ojt.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ojt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ojt_validation.pdf.gz | 726.4 KB | Display | wwPDB validaton report |
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Full document | 4ojt_full_validation.pdf.gz | 726.4 KB | Display | |
Data in XML | 4ojt_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4ojt_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/4ojt ftp://data.pdbj.org/pub/pdb/validation_reports/oj/4ojt | HTTPS FTP |
-Related structure data
-Links
-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.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: jhp_0082, mtn, mtnN, pfs / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.798 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 19.97 / Stereochemistry target values: ML
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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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