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Yorodumi- PDB-6dux: 2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dux | ||||||
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Title | 2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella pneumoniae in Complex with NAD. | ||||||
Components | 6-phospho-alpha-glucosidase | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 6-phospho-alpha-glucosidase / NAD | ||||||
Function / homology | Function and homology information 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 | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Microbiol Resour Announc / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dux.cif.gz | 357.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dux.ent.gz | 297.5 KB | Display | PDB format |
PDBx/mmJSON format | 6dux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dux_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6dux_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6dux_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 6dux_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/6dux ftp://data.pdbj.org/pub/pdb/validation_reports/du/6dux | HTTPS FTP |
-Related structure data
Related structure data | 6dt3C 6dvvC 6dxnC 6e85C 6nauC 6nbgC 6ndiC 6wn5C 6wn8C 6x1lC 7rjjC 7tl5C 7tzpC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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
-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.) Klebsiella pneumoniae (bacteria) / Gene: aglB / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) magic References: UniProt: Q9AGA6, maltose-6'-phosphate glucosidase |
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-Non-polymers , 7 types, 370 molecules
#2: Chemical | #3: Chemical | ChemComp-LMR / ( | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-BCT / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.9 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 10.3 mg/ml, 0.01M Tris-HCl pH 8.3, 2mM NAD; Screen: Classics II (B11) 2.1M DL-malic acid pH 7.0; Cryo: Screen + 20% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
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: 46596 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.037 / Rrim(I) all: 0.109 / Rsym value: 0.102 / Χ2: 1.367 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 3 / Num. unique obs: 2254 / CC1/2: 0.854 / Rpim(I) all: 0.282 / Rrim(I) all: 0.832 / Rsym value: 0.782 / Χ2: 1.009 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→29.89 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.611 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 49.003 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→29.89 Å
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