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Yorodumi- PDB-4g41: Crystal structure of s-adenosylhomocysteine nucleosidase from str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g41 | ||||||
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Title | Crystal structure of s-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin | ||||||
Components | MTA/SAH nucleosidase | ||||||
Keywords | HYDROLASE / MIXED ALPHA/BETA / S-ADENOSYLHOMOCYSTEINE / CLEAVAGE | ||||||
Function / homology | Nucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 5'-DEOXY-5'-METHYLTHIOADENOSINE / : Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Ponniah, K. / Norris, G.E. / Anderson, B.F. / Brown, R.L. / Tyler, P.C. / Evans, G.B. / Frohlich, R. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of s-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin; Authors: Ponniah, K. / Norris, G.E. / Anderson, B.F. / Brown, R.L. / Tyler, P.C. / Evans, G.B. / Frohlich, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g41.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g41.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 4g41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/4g41 ftp://data.pdbj.org/pub/pdb/validation_reports/g4/4g41 | 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: 25198.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: ATCC 10782 / Gene: HMPREF0841_1463, mtn N, mtnN / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: E0PXI9, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase #2: Chemical | ChemComp-MTA / | #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: 2.01 Å3/Da / Density % sol: 38.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG MME 5000, 0.1M MES, 0.2M AMMONIUM SULPHATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 20, 2008 / Details: MIRRORS |
Radiation | Monochromator: OPTICS CAPILLIARY / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→20.62 Å / Num. all: 66215 / Num. obs: 66215 / % possible obs: 87.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.91 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.4 / % possible all: 21.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: S.AUREUS MTAN Resolution: 1.45→20.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.998 / SU ML: 0.039 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.078 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE ADDED IN THIER 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 mean: 15.251 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→20.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.448→1.485 Å / Total num. of bins used: 20
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