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Yorodumi- PDB-4p54: Crystal Structure of the Helicobacter pylori MTAN-D198N mutant wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p54 | ||||||
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Title | Crystal Structure of the Helicobacter pylori MTAN-D198N mutant with 5'-methylthioadenosine in the active site. | ||||||
Components | Aminodeoxyfutalosine 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ronning, D.R. / Mishra, V. | ||||||
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 | 4p54.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p54.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 4p54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/4p54 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/4p54 | HTTPS FTP |
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-Related structure data
Related structure data | 4ojtC 4oy3C 3nm6S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 25105.965 Da / Num. of mol.: 1 / Mutation: D198N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: mtnN, mtn, jhp_0082 / Plasmid: PET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q9ZMY2, adenosylhomocysteine nucleosidase |
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#2: Chemical | ChemComp-MTA / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.5 and 25 % (w/v) PEG-3350. |
-Data collection
Diffraction | Mean temperature: 100 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: Nov 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→24.73 Å / Num. obs: 32308 / % possible obs: 99.7 % / Redundancy: 10.8 % / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.63→1.67 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 3.3 / % possible all: 99.2 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NM6 Resolution: 1.65→24.73 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 15.5 / 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: 41.019 Å2 / ksol: 0.358 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.65→24.73 Å
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Refine LS restraints |
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LS refinement shell |
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