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Yorodumi- PDB-3eei: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocystein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eei | ||||||
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Title | Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from neisseria meningitidis in complex with methylthio-immucillin-A | ||||||
Components | 5-methylthioadenosine nucleosidase/S-adenosylhomocysteine nucleosidase | ||||||
Keywords | HYDROLASE / MTAN / 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE / Immucillin A / Glycosidase | ||||||
Function / homology | Function and homology information adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / cytosol Similarity search - Function | ||||||
Biological species | Neisseria meningitidis serogroup B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å | ||||||
Authors | Ho, M. / Rinaldo-matthis, A. / Brown, R.L. / Norris, G.E. / Tyler, P.C. / Furneaux, R.H. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from neisseria meningitidis in complex with methylthio-immucillin-A Authors: Ho, M. / Rinaldo-matthis, A. / Brown, R.L. / Norris, G.E. / Tyler, P.C. / Furneaux, R.H. / Almo, S.C. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eei.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eei.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 3eei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/3eei ftp://data.pdbj.org/pub/pdb/validation_reports/ee/3eei | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24724.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Gene: pfs / Production host: Escherichia coli (E. coli) References: UniProt: Q9K054, methylthioadenosine nucleosidase, 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: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.05 AMMONIUM SULFATE, 0.05 M BIS-TRIS, 30% V/V PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→30 Å / Num. obs: 39063 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Χ2: 1.037 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→29.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.835 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.54 Å2 / Biso mean: 32.412 Å2 / Biso min: 19.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.829 Å / Total num. of bins used: 20
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