[English] 日本語
![](img/lk-miru.gif)
- PDB-8pms: NADase from Aspergillus fumigatus with replaced C-terminus from N... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8pms | ||||||
---|---|---|---|---|---|---|---|
Title | NADase from Aspergillus fumigatus with replaced C-terminus from Neurospora crassa | ||||||
![]() | Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA | ||||||
![]() | HYDROLASE / NADase / NAD hydrolase / Ca-binding / homodimer / glycoprotein / extracellular | ||||||
Function / homology | Tuberculosis necrotizing toxin / Tuberculosis necrotizing toxin / NAD+ glycohydrolase / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / hydrolase activity / extracellular region / metal ion binding / ACRYLIC ACID / Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kallio, J.P. / Ferrario, E. / Stromland, O. / Ziegler, M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Novel Calcium-Binding Motif Stabilizes and Increases the Activity of Aspergillus fumigatus Ecto-NADase. Authors: Ferrario, E. / Kallio, J.P. / Stromland, O. / Ziegler, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 396.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 273.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 33.6 KB | Display | |
Data in CIF | ![]() | 44.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pmrC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26651.146 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: MIFTNAILVISALLPATVLS = signal sequence EDPQRLVPRNYGT at the C-terminus is from N.crassa NADase, replacing the original C-terminus of AfNADase DVLFQGPGHHHHHH = 3C protease site and His-tag Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q4WL81, NAD+ glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
---|
-Sugars , 4 types, 12 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: 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 |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 143 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/AKR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/AKR.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-AKR / #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.94 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: MgCl2, HEPES and Polyacrylic acid 5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.67 Å / Num. obs: 75255 / % possible obs: 99.81 % / Redundancy: 14.38 % / Biso Wilson estimate: 73.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08156 / Rpim(I) all: 0.02955 / Net I/σ(I): 14.38 |
Reflection shell | Resolution: 2.4→2.486 Å / Rmerge(I) obs: 2.137 / Num. unique obs: 7381 / CC1/2: 0.456 / Rpim(I) all: 0.7324 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→46.67 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|