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Yorodumi- PDB-4jwt: Crystal structure of a putative 5'-methylthioadenosine/S-adenosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jwt | ||||||
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Title | Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Sulfurimonas denitrificans DSM 1251 (Target NYSGRC-029304 ) | ||||||
Components | Methylthioadenosine nucleosidase | ||||||
Keywords | HYDROLASE / Sulfurimonas denitrificans / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / adenine / Structural genomics / NYSGRC / New York Structural Genomics Research Consortium / PSI-Biology | ||||||
Function / homology | Function and homology information nucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from methylthioadenosine Similarity search - Function | ||||||
Biological species | Sulfurimonas denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Sampathkumar, P. / 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 Sulfurimonas denitrificans DSM 1251 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. / Suarez, J. / 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 | 4jwt.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jwt.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jwt_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 4jwt_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 4jwt_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4jwt_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/4jwt ftp://data.pdbj.org/pub/pdb/validation_reports/jw/4jwt | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28637.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfurimonas denitrificans (bacteria) / Strain: DSM 1251 / Gene: Suden_1392 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL References: UniProt: Q30QR2, methylthioadenosine nucleosidase | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ADE / | #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: 3.54 Å3/Da / Density % sol: 65.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG3 #84; 0.1 M Sodium Acetate:HCl pH 4.6, 2.0 M Sodium Formate ); Cryoprotection (33% Ethylene glycol), VAPOR ...Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG3 #84; 0.1 M Sodium Acetate:HCl pH 4.6, 2.0 M Sodium Formate ); Cryoprotection (33% Ethylene glycol), 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: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2013 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 26487 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 26.75 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 23.1 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 5.42 / Num. unique all: 1283 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→43.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.987 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. AUTHORS NOTE AN ELECTRON DENSITY FEATURE JUST BELOW ADENINE, WHICH COULD NOT BE SATISFACTORILY EXPLAINED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. AUTHORS NOTE AN ELECTRON DENSITY FEATURE JUST BELOW ADENINE, WHICH COULD NOT BE SATISFACTORILY EXPLAINED WITH BUFFER OR CRYSTALLIZATION COMPONENTS.
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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: 113.73 Å2 / Biso mean: 38.1574 Å2 / Biso min: 20.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→43.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.052→2.105 Å / Total num. of bins used: 20
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