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Yorodumi- PDB-5kb3: 1.4 A resolution structure of Helicobacter Pylori MTAN in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kb3 | |||||||||
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Title | 1.4 A resolution structure of Helicobacter Pylori MTAN in complexed with p-ClPh-DADMe-ImmA | |||||||||
Components | Aminodeoxyfutalosine nucleosidase | |||||||||
Keywords | HYDROLASE / nucleosidase / helicobacter pylori / neutron crystallography | |||||||||
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: 1.399 Å | |||||||||
Authors | Banco, M.T. / Ronning, D.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states. Authors: Banco, M.T. / Mishra, V. / Ostermann, A. / Schrader, T.E. / Evans, G.B. / Kovalevsky, A. / 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 | 5kb3.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kb3.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 5kb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kb3_validation.pdf.gz | 737.7 KB | Display | wwPDB validaton report |
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Full document | 5kb3_full_validation.pdf.gz | 738.8 KB | Display | |
Data in XML | 5kb3_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 5kb3_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/5kb3 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/5kb3 | HTTPS FTP |
-Related structure data
Related structure data | 5ccdC 5cceC 5jpcC 5k1zC 3nm5S C: citing same article (ref.) S: Starting model for refinement |
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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: 24975.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain J99 / ATCC 700824) (bacteria) Strain: J99 / ATCC 700824 / Gene: mtnN, mtn, jhp_0082 / Production host: Escherichia coli (E. coli) References: UniProt: Q9ZMY2, aminodeoxyfutalosine nucleosidase, adenosylhomocysteine nucleosidase |
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#2: Chemical | ChemComp-4CT / ( |
#3: Chemical | ChemComp-MG / |
#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: 52.01 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 100 mM HEPES pH 7.5, 18 % w/v polyethylene glycol 550 monomethyl ether, and 95 mM magnesium chloride hexahydrate. |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.399→34.76 Å / Num. obs: 50579 / % possible obs: 99.3 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.445 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NM5 Resolution: 1.399→34.76 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.51 / 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: 1.399→34.76 Å
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Refine LS restraints |
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LS refinement shell |
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