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Yorodumi- PDB-3nv7: Crystal structure of H.pylori phosphopantetheine adenylyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nv7 | ||||||
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Title | Crystal structure of H.pylori phosphopantetheine adenylyltransferase mutant I4V/N76Y | ||||||
Components | Phosphopantetheine adenylyltransferase | ||||||
Keywords | TRANSFERASE / Helicobacter pylori 26695 strain / mutant I4V/N76Y / phosphopantetheine adenylyltransferase | ||||||
Function / homology | Function and homology information pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Chen, C.H. / Cheng, C.S. / Yin, H.S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of H.pylori phosphopantetheine adenylyltransferase mutant I4V/N76Y Authors: Chen, C.H. / Cheng, C.S. / Yin, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nv7.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nv7.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 3nv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nv7_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 3nv7_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 3nv7_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 3nv7_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/3nv7 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/3nv7 | HTTPS FTP |
-Related structure data
Related structure data | 1h1tS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17726.623 Da / Num. of mol.: 1 / Mutation: I4V, N76Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: coaD, kdtB, HP_1475 / Production host: Escherichia coli (E. coli) References: UniProt: O26010, pantetheine-phosphate adenylyltransferase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACY / | #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: 2.54 Å3/Da / Density % sol: 51.54 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.5 Details: 10% PEG 4000, 0.1M sodium acetate, 0.2M Li2SO4, pH 5.5, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 18626 |
Reflection shell | Resolution: 1.75→1.81 Å / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H1T Resolution: 1.75→23.98 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.788 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / 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 max: 122.82 Å2 / Biso mean: 31.2635 Å2 / Biso min: 16.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→23.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.749→1.794 Å / Total num. of bins used: 20
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