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- PDB-9ouf: Crystal structure of an ADP-ribosyl hydrolase from Streptococcus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9ouf | ||||||
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Title | Crystal structure of an ADP-ribosyl hydrolase from Streptococcus parasanguinis | ||||||
![]() | Ribonuclease | ||||||
![]() | HYDROLASE / ADP-ribosyl Cyclase/hydrolase / toxin / antibacterial | ||||||
Function / homology | : / LXG domain / LXG domain profile. / Hydrolases; Acting on ester bonds / hydrolase activity / Ribonuclease![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Colautti, J. / Kim, Y. / Whitney, J.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Antibacterial ADP-ribosyl cyclase toxins inhibit bacterial growth by rapidly depleting NAD(P). Authors: Colautti, J. / Kim, Y. / Whitney, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.9 KB | Display | ![]() |
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PDB format | ![]() | 55.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.9 KB | Display | ![]() |
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Full document | ![]() | 436.8 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Components
#1: Protein | Mass: 17802.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A6N3DPK9, Hydrolases; Acting on ester bonds | ||||||
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#2: Chemical | ChemComp-EDO / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M ammonium acetate, 0.1 M BisTrisHCl pH 5.5, 17 % PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2025 |
Radiation | Monochromator: horizontal bounce Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→33.18 Å / Num. obs: 28170 / % possible obs: 99.4 % / Redundancy: 11.2 % / Biso Wilson estimate: 14.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.052 / Rrim(I) all: 0.129 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.39→1.46 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.271 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3879 / CC1/2: 0.576 / Rpim(I) all: 0.64 / Rrim(I) all: 1.429 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→33.18 Å
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Refine LS restraints |
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LS refinement shell |
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