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- PDB-4ocu: N-acetylhexosamine 1-phosphate kinase_ATCC15697 in complex with GlcNAc -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ocu | |||||||||
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Title | N-acetylhexosamine 1-phosphate kinase_ATCC15697 in complex with GlcNAc | |||||||||
![]() | N-acetylhexosamine 1-phosphate kinase | |||||||||
![]() | TRANSFERASE / kinaase | |||||||||
Function / homology | Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Aminoglycoside phosphotransferase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, T.L. / Wang, K.C. / Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. | |||||||||
![]() | ![]() Title: Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple reaction complexes. Authors: Wang, K.C. / Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. / Li, T.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.1 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.4 KB | Display | ![]() |
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Full document | ![]() | 462.5 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ocjSC ![]() 4ockC ![]() 4ocoC ![]() 4ocpC ![]() 4ocqC ![]() 4ocvC 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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Unit cell |
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Components
#1: Protein | Mass: 42536.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12 Gene: BLIJ_2250, Blon_2173 / Production host: ![]() ![]() | ||
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#2: Sugar | ChemComp-NDG / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.5 M lithium sulfate, 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2012 |
Radiation | Monochromator: Horizontally focusing single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.904→30 Å / Num. all: 34696 / Num. obs: 34696 / % possible obs: 99.74 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 36.43 |
Reflection shell | Resolution: 1.904→1.97 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 7.89 / Rsym value: 0.449 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4OCJ Resolution: 1.904→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.309 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.131 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.923 Å2
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Refinement step | Cycle: LAST / Resolution: 1.904→30 Å
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Refine LS restraints |
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