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- PDB-8ur1: Crystal structure N-acetylneuraminate lyase (NanA) from Klebsiell... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ur1 | ||||||
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Title | Crystal structure N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate bound halide free active site) | ||||||
![]() | 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 / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate bound halide free active site) Authors: Lovell, S. / Liu, L. / Seibold, S. / Mian, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.6 KB | Display | ![]() |
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PDB format | ![]() | 104.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.4 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.3 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: 33738.566 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 , 7 types, 191 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | ChemComp-1PE / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus C11: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4 KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to ...Details: Morpheus C11: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4 KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein prior to crystallization. Cryo: direct. This structure has no halides near KPI 165 in the active which resulted in movement of a nearby loop is the previous structures. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Sep 26, 2023 |
Radiation | Monochromator: HELIOS MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.93 Å / Num. obs: 33838 / % possible obs: 100 % / Redundancy: 42.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.036 / Rrim(I) all: 0.232 / Χ2: 0.94 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 30.7 % / Rmerge(I) obs: 1.93 / Num. measured all: 82554 / Num. unique obs: 2690 / CC1/2: 0.789 / Rpim(I) all: 0.354 / Rrim(I) all: 1.963 / Χ2: 0.77 / Net I/σ(I) obs: 2 |
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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: 2.1→46.93 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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