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Yorodumi- PDB-4u94: Structure of mycobacterial maltokinase, the missing link in the e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u94 | |||||||||||||||
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Title | Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway | |||||||||||||||
Components | Maltokinase | |||||||||||||||
Keywords | TRANSFERASE / Mycobacterium vanbalenii / Maltokinase / Maltose / Glycogen / AppCp | |||||||||||||||
Function / homology | Function and homology information maltokinase / trehalose biosynthetic process / carbohydrate phosphorylation / glycogen biosynthetic process / kinase activity / ATP binding Similarity search - Function | |||||||||||||||
Biological species | Mycobacterium vanbaalenii (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.473 Å | |||||||||||||||
Authors | Fraga, J. / Empadinhas, N. / Pereira, P.J.B. / Macedo-Ribeiro, S. | |||||||||||||||
Funding support | Portugal, 4items
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Citation | Journal: Sci Rep / Year: 2015 Title: Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway. Authors: Fraga, J. / Maranha, A. / Mendes, V. / Pereira, P.J. / Empadinhas, N. / Macedo-Ribeiro, S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u94.cif.gz | 203 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u94.ent.gz | 161.2 KB | Display | PDB format |
PDBx/mmJSON format | 4u94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u94_validation.pdf.gz | 423.9 KB | Display | wwPDB validaton report |
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Full document | 4u94_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 4u94_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 4u94_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/4u94 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/4u94 | HTTPS FTP |
-Related structure data
-Links
-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
#1: Protein | Mass: 49746.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium vanbaalenii (bacteria) / Strain: DSM 7251 / PYR-1 / Gene: mak, Mvan_5735 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A1TH50, maltokinase |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MOPS/sodium HEPES pH 7.5, 0.12 M ethylene glycols (0.03M each of di-ethyleneglycol, tri-ethyleneglycol, tetra-ethyleneglycol, and penta-ethyleneglycol), 30% PEG 500MME/PEG 20K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→40.741 Å / Num. obs: 84256 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rsym value: 0.057 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 7.7 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.473→40.741 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.473→40.741 Å
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Refine LS restraints |
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LS refinement shell |
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