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Yorodumi- PDB-5bvc: Crystal structure of Lipomyces starkeyi levoglucosan kinase bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bvc | ||||||
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Title | Crystal structure of Lipomyces starkeyi levoglucosan kinase bound to ADP, magnesium and levoglucosan in an alternate orientation. | ||||||
Components | Levoglucosan kinase | ||||||
Keywords | TRANSFERASE / SUGAR KINASE / ATP-BINDING / CARBOHYDRATE METABOLISM / LEVOGLUCOSAN | ||||||
Function / homology | Function and homology information 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 | Lipomyces starkeyi (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bacik, J.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bvc.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bvc.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 5bvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/5bvc ftp://data.pdbj.org/pub/pdb/validation_reports/bv/5bvc | HTTPS FTP |
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-Related structure data
Related structure data | 4yh5SC 4zfvC 4zluC 5bsbC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49395.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lipomyces starkeyi (fungus) / Production host: Escherichia coli (E. coli) References: UniProt: B3VI55, Transferases; Transferring phosphorus-containing groups |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-4PW / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.72 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: Equal amounts of LGK (25 mg/ml) in crystallization buffer (100 mM NaCl, 0.5 mM TCEP, 20 mM Tris pH 7.5, 2 mM ADP, 4 mM MgCl, 1 mM aluminum nitrate and 10 mM sodium fluoride) and ...Details: Equal amounts of LGK (25 mg/ml) in crystallization buffer (100 mM NaCl, 0.5 mM TCEP, 20 mM Tris pH 7.5, 2 mM ADP, 4 mM MgCl, 1 mM aluminum nitrate and 10 mM sodium fluoride) and crystallization buffer (1.3 M sodium malonate, 0.093 M Bis-Tris Propane pH 7.0) were mixed and and a resultant crystal was soaked with 200 mM levoglucosan. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.27 Å / Num. obs: 44939 / % possible obs: 98.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YH5 Resolution: 2→43.27 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.92 / 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: 2→43.27 Å
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Refine LS restraints |
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LS refinement shell |
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