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- PDB-8r17: Crystal structure of Neurospora crassa NADase with modified C-terminus -
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Open data
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Basic information
Entry | Database: PDB / ID: 8r17 | ||||||
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Title | Crystal structure of Neurospora crassa NADase with modified C-terminus | ||||||
![]() | Conidial surface nicotinamide adenine dinucleotide glycohydrolase,Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA | ||||||
![]() | HYDROLASE / NADase / NAD hydrolase / homodimer / glycoprotein / extracellular / TNT domain | ||||||
Function / homology | Tuberculosis necrotizing toxin / Tuberculosis necrotizing toxin / NAD+ glycohydrolase / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / hydrolase activity / extracellular region / metal ion binding / Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA / Conidial surface nicotinamide adenine dinucleotide glycohydrolase![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kallio, J.P. / Ferrario, E. / Ziegler, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Evolution of fungal tuberculosis necrotizing toxin (TNT) domain-containing enzymes reveals divergent adaptations to enhance NAD cleavage. Authors: Ferrario, E. / Kallio, J.P. / Emdadi, M. / Stromland, O. / Rack, J.G.M. / Ziegler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.8 KB | Display | ![]() |
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PDB format | ![]() | 38.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 748.8 KB | Display | ![]() |
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Full document | ![]() | 750.8 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r15C 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28183.324 Da / Num. of mol.: 1 Mutation: 233-EDPQRLVPRNY-243 replaced by LDESEYDEKVEYSNPYTPGPNQ Source method: isolated from a genetically manipulated source Details: MKFTLLSTAVALLTSTAVA = signal sequence DVLFQGPGHHHHHH = 3C proteace cleavage site and HIS-tag 233-DESEYDEKVEYSNPYTPGPNQ-254 = engineered modification, sequence from AfNADase C- ...Details: MKFTLLSTAVALLTSTAVA = signal sequence DVLFQGPGHHHHHH = 3C proteace cleavage site and HIS-tag 233-DESEYDEKVEYSNPYTPGPNQ-254 = engineered modification, sequence from AfNADase C-terminus,MKFTLLSTAVALLTSTAVA = signal sequence DVLFQGPGHHHHHH = 3C proteace cleavage site and HIS-tag 233-DESEYDEKVEYSNPYTPGPNQ-254 = engineered modification, sequence from AfNADase C-terminus Source: (gene. exp.) ![]() ![]() ![]() Gene: NCU07948, nadA, AFUA_6G14470 / Strain: ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293 / Production host: ![]() ![]() References: UniProt: Q7S936, UniProt: Q4WL81, NAD+ glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds | ||||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
#3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: Bis-Tris pH 5.5-6.5, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 12, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.98 Å / Num. obs: 16949 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 75.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.018 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible obs: 99.9 % / Rmerge(I) obs: 1.828 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1626 / CC1/2: 0.442 / Rpim(I) all: 0.666 |
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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: 83.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→43.94 Å
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Refine LS restraints |
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LS refinement shell |
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