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Yorodumi- PDB-5dk6: CRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dk6 | ||||||
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Title | CRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE (MTA/SAH) NUCLEOSIDASE (MTAN) FROM COLWELLIA PSYCHRERYTHRAEA 34H (CPS_4743, TARGET PSI-029300) IN COMPLEX WITH ADENINE AT 2.27 A RESOLUTION | ||||||
Components | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | ||||||
Keywords | HYDROLASE / MTA/SAH NUCLEOSIDASE FAMILY / MTAN / GAMMAPROTEOBACTERIA / Vibrio psychroerythus / ADENINE / PROTEIN-LIGAND COMPLEX / PROTEIN STRUCTURE INITIATIVE / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Function and homology information adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine Similarity search - Function | ||||||
Biological species | Colwellia psychrerythraea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å | ||||||
Authors | Himmel, D.M. / Bhosle, R. / Toro, R. / Ahmed, M. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. ...Himmel, D.M. / Bhosle, R. / Toro, R. / Ahmed, M. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R.D. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be published Title: CRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE (MTA/SAH)NUCLEOSIDASE (MTAN) FROM COLWELLIA PSYCHRERYTHRAEA 34H (CPS_4743, TARGET PSI-029300) IN COMPLEX WITH ADENINE AT 2.27 A RESOLUTION Authors: Himmel, D.M. / Bhosle, R. / Toro, R. / Ahmed, M. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / ...Authors: Himmel, D.M. / Bhosle, R. / Toro, R. / Ahmed, M. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R.D. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) #1: Journal: Biochemistry / Year: 2015 Title: Active site and remote contributions to catalysis in methylthioadenosine nucleosidases. Authors: Thomas, K. / Cameron, S.A. / Almo, S.C. / Burgos, E.S. / Gulab, S.A. / Schramm, V.L. #2: Journal: Nat. Chem. Biol. / Year: 2009 Title: Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing. Authors: Gutierrez, J.A. / Crowder, T. / Rinaldo-Matthis, A. / Ho, M.C. / 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 | 5dk6.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dk6.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dk6_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 5dk6_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 5dk6_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 5dk6_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/5dk6 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/5dk6 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28485.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: mtnN, CPS_4743 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q47UY5, adenosylhomocysteine nucleosidase |
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#2: Chemical | ChemComp-GLY / |
#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: 3.84 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein (37.95 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) were combined with an equal volume of Reservoir (100 mM Bicine pH 8.0, 1.98 M Ammonium Sulfate, ...Details: Protein (37.95 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) were combined with an equal volume of Reservoir (100 mM Bicine pH 8.0, 1.98 M Ammonium Sulfate, 135 mM Sodium Succinate, 4 mM Glycine, 15 mM CYMAL-7); Cryoprotection (75 mM Bicine pH 8.0, 1.49 M Ammonium Sulfate, 101 mM Sodium Succinate, 3 mM Glycine, 11 mM CYMAL-7) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 17, 2013 / Details: MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.9 % / Number: 143135 / Rmerge(I) obs: 0.1 / Χ2: 1 / D res high: 2.28 Å / D res low: 26 Å / Num. obs: 37023 / % possible obs: 96.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.268→26 Å / Num. obs: 37023 / % possible obs: 96.4 % / Observed criterion σ(I): -0.3 / Redundancy: 3.9 % / Biso Wilson estimate: 33.16 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.27→2.36 Å / Redundancy: 2 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.148 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.27→25.28 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 22.27 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.6 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→25.28 Å
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Refine LS restraints |
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LS refinement shell |
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