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Yorodumi- PDB-7vt9: CRYSTAL STRUCTURE AT 3.4 ANGSTROMS RESOLUTION OF Maltodextrin glu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vt9 | |||||||||
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Title | CRYSTAL STRUCTURE AT 3.4 ANGSTROMS RESOLUTION OF Maltodextrin glucosidase, MalZ, FROM Escherichia coli | |||||||||
Components | Maltodextrin glucosidase | |||||||||
Keywords | HYDROLASE / Alpha-amylase / Maltodextrin glucosidase | |||||||||
Function / homology | Function and homology information alpha-glucan catabolic process / alpha-1,4-glucosidase activity / maltose alpha-glucosidase activity / alpha-glucosidase / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Ahn, W.-C. / Ahn, Y. / Woo, E.-J. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Dimeric architecture of maltodextrin glucosidase (MalZ) provides insights into the substrate recognition and hydrolysis mechanism. Authors: Ahn, W.C. / An, Y. / Song, K.M. / Park, K.H. / Lee, S.J. / Oh, B.H. / Park, J.T. / Woo, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vt9.cif.gz | 771.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vt9.ent.gz | 609.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/7vt9 ftp://data.pdbj.org/pub/pdb/validation_reports/vt/7vt9 | HTTPS FTP |
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-Related structure data
Related structure data | 2d0gS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 604 / Label seq-ID: 1 - 604
NCS oper: (Code: givenMatrix: (0.0246912371563, -0.999667243429, 0.00746627230298), (-0.999665315024, -0.0247474881892, -0.0075378887199), (0.00772015192353, -0.00727765365577, -0.999943715922)Vector: ...NCS oper: (Code: given Matrix: (0.0246912371563, -0.999667243429, 0.00746627230298), Vector: |
-Components
#1: Protein | Mass: 70406.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: malZ, b0403, JW0393 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P21517, alpha-glucosidase #2: 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: 5.05 Å3/Da / Density % sol: 75.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% polyacrylic acid 5100, 100 mM HEPES/Sodium hydroxide pH 7.0 and 20 mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 2, 2013 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→40.91 Å / Num. obs: 43678 / % possible obs: 99.9 % / Redundancy: 25.4 % / Biso Wilson estimate: 80.22 Å2 / Rmerge(I) obs: 0.355 / Net I/σ(I): 4.02 |
Reflection shell | Resolution: 3.3→3.418 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.001 / Num. unique obs: 4169 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D0G Resolution: 3.3→40.91 Å / SU ML: 0.6527 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.0566 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→40.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.25651080492 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.5358538903 Å / Origin y: -23.6310403161 Å / Origin z: -68.7830396425 Å
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Refinement TLS group | Selection details: all |