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Yorodumi- PDB-8rvk: Maltodextrin phosphorylase (MalP) in complex with a alpha-1,2-cyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rvk | ||||||
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Title | Maltodextrin phosphorylase (MalP) in complex with a alpha-1,2-cyclophellitol analogue | ||||||
Components | Maltodextrin phosphorylase | ||||||
Keywords | TRANSFERASE / Phosphorylase / Glycosyltransferase / GT35 / Carbohydrate Metabolism | ||||||
Function / homology | Function and homology information maltodextrin phosphorylase activity / alpha-glucan catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Bennett, M. / Ofman, T.P. / Overkleeft, H.S. / Davies, G.J. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Chemistry / Year: 2024 Title: Conformational and Electronic Variations in 1,2- and 1,5a-Cyclophellitols and their Impact on Retaining alpha-Glucosidase Inhibition. Authors: Ofman, T.P. / Heming, J.J.A. / Nin-Hill, A. / Kullmer, F. / Moran, E. / Bennett, M. / Steneker, R. / Klein, A.M. / Ruijgrok, G. / Kok, K. / Armstrong, Z.W.B. / Aerts, J.M.F.G. / van der ...Authors: Ofman, T.P. / Heming, J.J.A. / Nin-Hill, A. / Kullmer, F. / Moran, E. / Bennett, M. / Steneker, R. / Klein, A.M. / Ruijgrok, G. / Kok, K. / Armstrong, Z.W.B. / Aerts, J.M.F.G. / van der Marel, G.A. / Rovira, C. / Davies, G.J. / Artola, M. / Codee, J.D.C. / Overkleeft, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rvk.cif.gz | 358.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rvk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/8rvk ftp://data.pdbj.org/pub/pdb/validation_reports/rv/8rvk | HTTPS FTP |
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-Related structure data
Related structure data | 8rw3C C: citing same article (ref.) |
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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: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 796 / Label seq-ID: 3 - 796
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 90869.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: malP, b3417, JW5689 / Production host: Escherichia coli (E. coli) / References: UniProt: P00490, glycogen phosphorylase |
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-Non-polymers , 5 types, 687 molecules
#2: Chemical | ChemComp-A1H3V / ( Mass: 203.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO5 / Feature type: SUBJECT OF INVESTIGATION | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2-0.5 M Li2SO4 monohydrate, 0.1 M Bis-Tris pH 5.5-7.0 and 25-30% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→71.503 Å / Num. obs: 160021 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.992 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.89→1.92 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 7599 / CC1/2: 0.284 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→71.503 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.187 / SU ML: 0.172 / Cross valid method: NONE / ESU R: 0.204 / ESU R Free: 0.182 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.046 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→71.503 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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