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Yorodumi- PDB-4jos: Crystal structure of a putative 5'-methylthioadenosine/S-adenosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jos | ||||||
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Title | Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Francisella philomiragia ATCC 25017 (Target NYSGRC-029335) | ||||||
Components | Adenosylhomocysteine nucleosidase | ||||||
Keywords | HYDROLASE / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / adenine / Structural genomics / NYSGRC / New York Structural Genomics Research Consortium / PSI-Biology | ||||||
Function / homology | Function and homology information adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from methylthioadenosine Similarity search - Function | ||||||
Biological species | Francisella philomiragia subsp. philomiragia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Sampathkumar, P. / Schramm, V.L. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: to be published Title: Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Francisella philomiragia ATCC 25017 (Target NYSGRC-029335) Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / ...Authors: Sampathkumar, P. / Gizzi, A. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Morisco, L.L. / Sojitra, S.S. / Wasserman, S.R. / Haapalainen, A. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Schramm, V.L. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jos.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jos.ent.gz | 94.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/4jos ftp://data.pdbj.org/pub/pdb/validation_reports/jo/4jos | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27995.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella philomiragia subsp. philomiragia (bacteria) Strain: ATCC 25017 / Gene: Fphi_0356 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL References: UniProt: B0TZL4, adenosylhomocysteine nucleosidase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 2.14 Å3/Da / Density % sol: 42.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG1 #13; G10: 0.6 M Sodium Chloride, 0.1 M MES:NaOH pH 6.5, 20% (w/v) PEG 4000 )); Cryoprotection (30% Ethylene ...Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG1 #13; G10: 0.6 M Sodium Chloride, 0.1 M MES:NaOH pH 6.5, 20% (w/v) PEG 4000 )); Cryoprotection (30% Ethylene glycol), temperature 298K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 14, 2013 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 85555 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.119 / Net I/σ(I): 21.06 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 2.88 / Num. unique all: 4211 / Rsym value: 0.847 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→29.06 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 0.923 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: IN BOTH A AND B SUBUNITS, AUTHORS HAVE NOTED AN ELECTRON DENSITY FEATURE JUST BELOW ADENINE. THESE DENSITIES WERE LEFT UNEXPLAINED AS THEY DO NOT APPEAR TO BE CORRESPONDING TO ANY COMPONENTS ...Details: IN BOTH A AND B SUBUNITS, AUTHORS HAVE NOTED AN ELECTRON DENSITY FEATURE JUST BELOW ADENINE. THESE DENSITIES WERE LEFT UNEXPLAINED AS THEY DO NOT APPEAR TO BE CORRESPONDING TO ANY COMPONENTS BUFFER OR CRYSTALLIZATION REAGENT. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.72 Å2 / Biso mean: 16.2734 Å2 / Biso min: 7.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→29.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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