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- PDB-7n1s: Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n1s | ||||||
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Title | Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase | ||||||
![]() | Phosphodiesterase-nucleotide pyrophosphatase | ||||||
![]() | HYDROLASE / enzyme / nucleotide / pyrophosphatase / phosphodiesterase / bacterial | ||||||
Function / homology | Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline-phosphatase-like, core domain superfamily / transferase activity / hydrolase activity / Alkaline phosphatase family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Fernandez, D. / Li, L. / Brown, J.A. / Carozza, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: ENPP1's regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating STING signaling. Authors: Carozza, J.A. / Cordova, A.F. / Brown, J.A. / AlSaif, Y. / Bohnert, V. / Cao, X. / Mardjuki, R.E. / Skariah, G. / Fernandez, D. / Li, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.9 KB | Display | ![]() |
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PDB format | ![]() | 125 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 39.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mw8C ![]() 2gsuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 45 - 425 / Label seq-ID: 2 - 382
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Components
#1: Protein | Mass: 41749.039 Da / Num. of mol.: 2 / Mutation: H214A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2018 Details: Rh coated collimating mirrors, K-B focusing mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→66.606 Å / Num. all: 45218 / Num. obs: 45218 / % possible obs: 100 % / Redundancy: 7.3 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.109 / Rsym value: 0.101 / Net I/av σ(I): 4.9 / Net I/σ(I): 9.7 / Num. measured all: 328450 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GSU Resolution: 2→30.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2386 / WRfactor Rwork: 0.1957 / FOM work R set: 0.7108 / SU B: 7.608 / SU ML: 0.193 / SU R Cruickshank DPI: 0.2435 / SU Rfree: 0.1945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.194 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.41 Å2 / Biso mean: 44.528 Å2 / Biso min: 23.99 Å2
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Refinement step | Cycle: final / Resolution: 2→30.61 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 45434 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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