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- PDB-6fv3: Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fv3 | |||||||||||||||||||||
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Title | Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase from Mycobacterium smegmatis. | |||||||||||||||||||||
![]() | N-acetylglucosamine-6-phosphate deacetylase | |||||||||||||||||||||
![]() | HYDROLASE / N-acetyl-D-glucosamine-6-phosphate mycobacteria / carbohydrate metabolism | |||||||||||||||||||||
Function / homology | ![]() N-acetylglucosamine-6-phosphate deacetylase / N-acetylgalactosamine-6-phosphate deacetylase activity / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine metabolic process / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Ahangar, M.S. / Furze, C.M. / Guy, C.S. / Cooper, C. / Maskew, K.S. / Graham, B. / Cameron, A.D. / Fullam, E. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional determination of homologs of theMycobacterium tuberculosis N-acetylglucosamine-6-phosphate deacetylase (NagA). Authors: Ahangar, M.S. / Furze, C.M. / Guy, C.S. / Cooper, C. / Maskew, K.S. / Graham, B. / Cameron, A.D. / Fullam, E. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.4 KB | Display | ![]() |
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PDB format | ![]() | 226.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 4.2 MB | Display | ![]() |
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Full document | ![]() | 4.3 MB | Display | |
Data in XML | ![]() | 54.1 KB | Display | |
Data in CIF | ![]() | 75.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fv4C ![]() 2p50S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41316.746 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 / Gene: nagA, MSMEG_2119 / Production host: ![]() ![]() References: UniProt: A0QU89, N-acetylglucosamine-6-phosphate deacetylase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion Details: NagA crystals grew in a condition containing 0.12 M monosaccharide mix (Morpheus, Molecular Dimensions), 0.1 M imidazole/MES pH 6.5, 20 % PEG 500 MME, 10 % w/v PEG 20000 with the addition of ...Details: NagA crystals grew in a condition containing 0.12 M monosaccharide mix (Morpheus, Molecular Dimensions), 0.1 M imidazole/MES pH 6.5, 20 % PEG 500 MME, 10 % w/v PEG 20000 with the addition of 10 mM CdCl2 additive. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→55.23 Å / Num. obs: 51044 / % possible obs: 98.2 % / Redundancy: 2.6 % / CC1/2: 0.96 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.173 / Rrim(I) all: 0.245 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.58→2.6296 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 1 / Num. unique obs: 555 / CC1/2: 0.434 / Rpim(I) all: 0.902 / Rrim(I) all: 0.059 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2P50 Resolution: 2.58→51.951 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→51.951 Å
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Refine LS restraints |
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LS refinement shell |
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