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Yorodumi- PDB-2o5w: Structure of the E. coli dihydroneopterin triphosphate pyrophosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o5w | ||||||
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Title | Structure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase in complex with Sm+3 and pyrophosphate | ||||||
Components | dATP pyrophosphohydrolase | ||||||
Keywords | HYDROLASE / dihydroneopterin triphosphate pyrophosphohydrolase nudix nucleoside triphosphate pyrophosphohydrolase mutt | ||||||
Function / homology | Function and homology information dihydroneopterin triphosphate diphosphatase / dihydroneopterin triphosphate pyrophosphohydrolase activity / dATP diphosphatase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.6 Å | ||||||
Authors | Gabelli, S.B. / Bianchet, M.A. / Amzel, L.M. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis. Authors: Gabelli, S.B. / Bianchet, M.A. / Xu, W. / Dunn, C.A. / Niu, Z.D. / Amzel, L.M. / Bessman, M.J. #1: Journal: J.Biol.Chem. / Year: 1996 Title: Escherichia coli orf17 codes for a nucleoside triphosphate pyrophosphohydrolase member of the mutt family of proteins Authors: O'Handley, S.F. / Frick, D.N. / Bullions, L.C. / Mildvan, A.S. / Bessman, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o5w.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o5w.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 2o5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o5w_validation.pdf.gz | 478.1 KB | Display | wwPDB validaton report |
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Full document | 2o5w_full_validation.pdf.gz | 486.4 KB | Display | |
Data in XML | 2o5w_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 2o5w_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/2o5w ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o5w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 17327.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nudB, ntpA / Plasmid: pet11b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: P0AFC0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Non-polymers , 5 types, 80 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 1.89 Å3/Da / Density % sol: 34.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 1.3-1.5 AMMONIUM SULFATE, 1% PROPANOL, 3-5 MM DTT, 4MM SODIUM PYROPHOSPHATE, 100MM NA HEPES, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.97 Å / Num. obs: 14304 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.096 |
Reflection shell | Resolution: 2.6→2.67 Å / Rsym value: 0.326 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.6→19.97 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.867 / SU B: 15.321 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: 35.097 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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