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Yorodumi- PDB-2gsu: Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gsu | ||||||
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Title | Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with AMP | ||||||
Components | phosphodiesterase-nucleotide pyrophosphatase | ||||||
Keywords | HYDROLASE / Alpha Beta / NPP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Xanthomonas axonopodis pv. citri str. 306 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Zalatan, J.G. / Fenn, T.D. / Brunger, A.T. / Herschlag, D. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution Authors: Zalatan, J.G. / Fenn, T.D. / Brunger, A.T. / Herschlag, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gsu.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gsu.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gsu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gsu ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gsu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: THR / End label comp-ID: MET / Refine code: 4 / Auth seq-ID: 44 - 425 / Label seq-ID: 5 - 386
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Details | Dimer in asymmetric unit, likely functional as a monomer |
-Components
#1: Protein | Mass: 42741.086 Da / Num. of mol.: 2 / Fragment: Residues (44-425) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri str. 306 (bacteria) Species: Xanthomonas axonopodisCitrus canker / Strain: pv. citri str. 306 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PIS1, nucleotide diphosphatase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 1.99 Å3/Da / Density % sol: 38.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Bis-Tris HCl, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2005 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 41903 / Num. obs: 41903 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.142 |
Reflection shell | Resolution: 2→2.05 Å / % possible all: 60.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→46.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 16.185 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.256 / Stereochemistry target values: Engh & Huber / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.653 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5657 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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