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- PDB-8u90: Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8u90 | |||||||||
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Title | Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (Apo, hexagonal form) | |||||||||
![]() | N-acetylneuraminate lyase | |||||||||
![]() | LIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / N-acetylneuraminate lyase | |||||||||
Function / homology | ![]() N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (Apo, hexagonal form) Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140 KB | Display | ![]() |
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PDB format | ![]() | 106.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.6 KB | Display | ![]() |
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Full document | ![]() | 432.4 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.7 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33669.527 Da / Num. of mol.: 1 / Mutation: V93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: nanA / Plasmid: KlaeA.01563.a.B1 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 263 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus B7: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM HEPES/MOPS, pH 7.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein ...Details: Morpheus B7: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM HEPES/MOPS, pH 7.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein prior to crystallization. Plate 13191 well B7 drop 1. Puck: PSL-1302, Cryo: direct |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 20, 2023 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.8 Å / Num. obs: 50082 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.016 / Rrim(I) all: 0.099 / Χ2: 0.99 / Net I/σ(I): 28.4 / Num. measured all: 1963723 |
Reflection shell | Resolution: 1.85→1.89 Å / % possible obs: 99.9 % / Redundancy: 37.9 % / Rmerge(I) obs: 2.685 / Num. measured all: 113941 / Num. unique obs: 3009 / CC1/2: 0.911 / Rpim(I) all: 0.44 / Rrim(I) all: 2.722 / Χ2: 0.95 / Net I/σ(I) obs: 1.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→35.94 Å
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Refine LS restraints |
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LS refinement shell |
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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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