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Yorodumi- PDB-4oy3: Crystal Structure of the Helicobacter pylori MTAN-D198N mutant wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oy3 | ||||||
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Title | Crystal Structure of the Helicobacter pylori MTAN-D198N mutant with S-Adenosylhomocysteine in the active site | ||||||
Components | Aminodeoxyfutalosine nucleosidase | ||||||
Keywords | HYDROLASE / Homodimer | ||||||
Function / homology | Function and homology information 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 | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 | 4oy3.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oy3.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 4oy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oy3_validation.pdf.gz | 698.4 KB | Display | wwPDB validaton report |
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Full document | 4oy3_full_validation.pdf.gz | 699.2 KB | Display | |
Data in XML | 4oy3_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 4oy3_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/4oy3 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/4oy3 | 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: 25105.965 Da / Num. of mol.: 1 / Fragment: UNP residues 2-230 / 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, aminodeoxyfutalosine nucleosidase, adenosylhomocysteine nucleosidase |
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#2: Chemical | ChemComp-SAH / |
#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: 2.52 Å3/Da / Density % sol: 51.15 % |
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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 pH 7.5 and 30 % (v/v) PEG-MME 550. |
-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 / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 75266 / % possible obs: 95 % / Redundancy: 10.9 % / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 4.1 / % possible all: 92.6 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1839) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→22.019 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.48 / 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: 1.2→22.019 Å
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Refine LS restraints |
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LS refinement shell |
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