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Yorodumi- PDB-3o4v: Crystal structure of E. coli MTA/SAH nucleosidase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o4v | ||||||
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Title | Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA | ||||||
Components | MTA/SAH nucleosidase | ||||||
Keywords | HYDROLASE / mixed alpha/beta dimer | ||||||
Function / homology | Function and homology information toxic metabolite repair / purine deoxyribonucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Siu, K.K.W. / Howell, P.L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA Authors: Siu, K.K.W. / Howell, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o4v.cif.gz | 110.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o4v.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 3o4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o4v_validation.pdf.gz | 1014.6 KB | Display | wwPDB validaton report |
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Full document | 3o4v_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3o4v_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 3o4v_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/3o4v ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o4v | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24612.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mtn, pfs / Plasmid: pPROEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: D3QWG1, UniProt: P0AF12*PLUS, adenosylhomocysteine nucleosidase, methylthioadenosine nucleosidase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-IPA / | #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: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.6 Details: 60 mM Sodium acetate, pH 4.6, 35% (v/v) isopropanol, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CONFOCAL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→32.93 Å / Num. obs: 46533 / % possible obs: 98.8 % / Redundancy: 12.31 % / Rmerge(I) obs: 0.049 / Χ2: 0.93 / Net I/σ(I): 29.5 / Scaling rejects: 30157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.75→21.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.83 Å2 / Biso mean: 14.5508 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→21.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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