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- PDB-6dvv: 2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dvv | ||||||
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Title | 2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella pneumoniae in Complex with NAD and Mn2+. | ||||||
![]() | 6-phospho-alpha-glucosidase | ||||||
![]() | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 6-phospho-alpha-glucosidase / NAD / Mn2+ | ||||||
Function / homology | ![]() maltose-6'-phosphate glucosidase / maltose-6'-phosphate glucosidase activity / sucrose metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae. Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 364.2 KB | Display | ![]() |
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PDB format | ![]() | 303 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 807.7 KB | Display | ![]() |
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Full document | ![]() | 813.6 KB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 52.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dt3C ![]() 6duxC ![]() 6dxnC ![]() 6e85C ![]() 6nauC ![]() 6nbgC ![]() 6ndiC ![]() 6wn5C ![]() 6wn8C ![]() 6x1lC ![]() 7rjjC ![]() 7tl5C ![]() 7tzpC C: citing same article ( |
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Similar structure data | |
Other databases |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50334.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9AGA6, maltose-6'-phosphate glucosidase |
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-Non-polymers , 7 types, 388 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAD / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 7.3 mg/ml, 0.01M Tris-HCl pH 8.3, 2mM Mn; Screen: Classics II (G4), 0.2M Lithium sulfate, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350; |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2018 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 47795 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.036 / Rrim(I) all: 0.099 / Rsym value: 0.092 / Χ2: 1.525 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2327 / CC1/2: 0.837 / Rpim(I) all: 0.324 / Rrim(I) all: 0.894 / Rsym value: 0.833 / Χ2: 0.991 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.294 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→28.99 Å
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