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- PDB-8rvk: Maltodextrin phosphorylase (MalP) in complex with a alpha-1,2-cyc... -

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Basic information

Entry
Database: PDB / ID: 8rvk
TitleMaltodextrin phosphorylase (MalP) in complex with a alpha-1,2-cyclophellitol analogue
ComponentsMaltodextrin phosphorylase
KeywordsTRANSFERASE / Phosphorylase / Glycosyltransferase / GT35 / Carbohydrate Metabolism
Function / homology
Function and homology information


maltodextrin phosphorylase activity / alpha-glucan catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site.
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Maltodextrin phosphorylase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsBennett, M. / Ofman, T.P. / Overkleeft, H.S. / Davies, G.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
CitationJournal: 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
DepositionFeb 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin phosphorylase
B: Maltodextrin phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,43460
Polymers181,7392
Non-polymers4,69558
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-179 kcal/mol
Surface area56460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.498, 119.79, 150.75
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

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

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Maltodextrin phosphorylase


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 / (3~{a}~{R},4~{R},5~{R},6~{R},7~{a}~{S})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3~{a},4,5,6,7,7~{a}-hexahydro-3~{H}-1,3-benzoxazol-2-one / alpha-1,2-cyclophellitol analogue


Mass: 203.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.89→1.92 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 7599 / CC1/2: 0.284 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata scaling
Cootmodel building
MOLREPphasing
xia2data reduction
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2294 1377 1.314 %
Rwork0.1773 103418 -
all0.178 --
obs-159923 99.992 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.046 Å2
Baniso -1Baniso -2Baniso -3
1-2.095 Å20 Å2-0 Å2
2---1.845 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.18→71.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12599 0 312 630 13541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01213177
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612237
X-RAY DIFFRACTIONr_angle_refined_deg2.3811.81417843
X-RAY DIFFRACTIONr_angle_other_deg0.8421.75828119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2551593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.4024.89677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.369102123
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.70410641
X-RAY DIFFRACTIONr_chiral_restr0.1320.21941
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023115
X-RAY DIFFRACTIONr_nbd_refined0.2320.22968
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.211773
X-RAY DIFFRACTIONr_nbtor_refined0.1930.26454
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.27262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2664
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0950.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.29
X-RAY DIFFRACTIONr_nbd_other0.2280.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2880.26
X-RAY DIFFRACTIONr_mcbond_it4.5893.4236372
X-RAY DIFFRACTIONr_mcbond_other4.5833.4236372
X-RAY DIFFRACTIONr_mcangle_it5.7416.1347965
X-RAY DIFFRACTIONr_mcangle_other5.7436.1357966
X-RAY DIFFRACTIONr_scbond_it5.8173.8136805
X-RAY DIFFRACTIONr_scbond_other5.6173.7826730
X-RAY DIFFRACTIONr_scangle_it7.7136.8149878
X-RAY DIFFRACTIONr_scangle_other7.3956.7579765
X-RAY DIFFRACTIONr_lrange_it8.26632.68115047
X-RAY DIFFRACTIONr_lrange_other8.26832.53814952
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.0526758
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.094750.05009
12AX-RAY DIFFRACTIONLocal ncs0.094750.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.18-2.2370.266970.2775600.2776570.9430.9421000.268
2.237-2.2980.287810.25674050.25774860.9330.9511000.251
2.298-2.3640.312850.24571940.24672790.9410.9561000.233
2.364-2.4370.2241010.21969440.21970460.9690.96699.98580.203
2.437-2.5170.288830.20267470.20368300.9490.9731000.182
2.517-2.6050.243820.20765690.20866520.9620.97299.9850.182
2.605-2.7030.268960.20963000.2163960.9560.9731000.181
2.703-2.8130.2241070.18360670.18461750.9680.97999.98380.154
2.813-2.9380.256980.17958050.1859030.9620.981000.15
2.938-3.0820.259640.18456480.18557120.9610.9781000.156
3.082-3.2480.211640.18553270.18553910.9740.981000.161
3.248-3.4440.272600.19750540.19851150.9540.97899.98050.177
3.444-3.6820.254550.1747840.17148390.9640.9851000.154
3.682-3.9760.202720.14644420.14745140.9780.9881000.129
3.976-4.3540.167550.12640990.12741540.9810.9911000.111
4.354-4.8660.174360.11637360.11737720.9820.9921000.105
4.866-5.6140.186470.13433280.13433750.9780.9911000.119
5.614-6.8650.193410.16428290.16428700.9790.9851000.143
6.865-9.6640.247340.15922270.1622610.9660.9831000.151
9.664-71.5030.218190.19813270.19813460.9670.9631000.199

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