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- PDB-4zfv: Lipomyces starkeyi levoglucosan kinase bound to ADP and magnesium. -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zfv | |||||||||
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Title | Lipomyces starkeyi levoglucosan kinase bound to ADP and magnesium. | |||||||||
![]() | Levoglucosan kinase | |||||||||
![]() | TRANSFERASE / Sugar kinase / ATP-binding / carbohydrate metabolism | |||||||||
Function / homology | ![]() levoglucosan kinase / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bacik, J.P. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Producing Glucose 6-Phosphate from Cellulosic Biomass: STRUCTURAL INSIGHTS INTO LEVOGLUCOSAN BIOCONVERSION. Authors: Bacik, J.P. / Klesmith, J.R. / Whitehead, T.A. / Jarboe, L.R. / Unkefer, C.J. / Mark, B.L. / Michalczyk, 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 | ![]() | 221.6 KB | Display | ![]() |
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PDB format | ![]() | 171.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.8 KB | Display | ![]() |
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Full document | ![]() | 783.2 KB | Display | |
Data in XML | ![]() | 45.7 KB | Display | |
Data in CIF | ![]() | 73.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yh5SC ![]() 4zluC ![]() 5bsbC ![]() 5bvcC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 49395.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B3VI55, Transferases; Transferring phosphorus-containing groups #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.05 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Equal volumes of reservoir buffer (22% polyethylene glycol (PEG) 4000, 0.1 M sodium acetate, 0.1 M Tris pH 7.5) and LGK (7 mg/ml) in crystallization buffer (50 mM NaCl, 2 mM ADP, 4 mM MgCl2 ...Details: Equal volumes of reservoir buffer (22% polyethylene glycol (PEG) 4000, 0.1 M sodium acetate, 0.1 M Tris pH 7.5) and LGK (7 mg/ml) in crystallization buffer (50 mM NaCl, 2 mM ADP, 4 mM MgCl2 , 0.5 mM TCEP, 20 mM Tris pH 7.5) were mixed. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.2 Å / Num. obs: 244767 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YH5 Resolution: 1.5→47.2 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→47.2 Å
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Refine LS restraints |
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LS refinement shell |
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