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- PDB-6yve: Glycogen phosphorylase b in complex with pelargonidin 3-O-beta-D-... -

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Basic information

Entry
Database: PDB / ID: 6yve
TitleGlycogen phosphorylase b in complex with pelargonidin 3-O-beta-D-glucoside
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
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
PYRIDOXAL-5'-PHOSPHATE / pelargonidin 3-O-beta-D-glucoside / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDrakou, C.E. / Gardeli, C. / Tsialtas, I. / Alexopoulos, S. / Mallouchos, A. / Koulas, S. / Tsagkarakou, A. / Asimakopoulos, D. / Leonidas, D.D. / Psarra, A.M. / Skamnaki, V.T.
CitationJournal: J.Agric.Food Chem. / Year: 2020
Title: Affinity Crystallography Reveals Binding of Pomegranate Juice Anthocyanins at the Inhibitor Site of Glycogen Phosphorylase: The Contribution of a Sugar Moiety to Potency and Its Implications to the Binding Mode.
Authors: Drakou, C.E. / Gardeli, C. / Tsialtas, I. / Alexopoulos, S. / Mallouchos, A. / Koulas, S.M. / Tsagkarakou, A.S. / Asimakopoulos, D. / Leonidas, D.D. / Psarra, A.G. / Skamnaki, V.T.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1824
Polymers97,4221
Non-polymers7603
Water7,710428
1
AAA: Glycogen phosphorylase, muscle form
hetero molecules

AAA: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3648
Polymers194,8452
Non-polymers1,5196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area6080 Å2
ΔGint-18 kcal/mol
Surface area57050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.147, 126.147, 115.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-1402-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form / / Myophosphorylase


Mass: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PUQ / pelargonidin 3-O-beta-D-glucoside / (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[[2-(4-hydroxyphenyl)-5,7-bis(oxidanyl)-2~{H}-chromen-3-yl]oxy]oxane-3,4,5-triol


Mass: 434.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22O10 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 6.8 / Details: 10mM BES buffer pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→126.15 Å / Num. obs: 54889 / % possible obs: 99.9 % / Redundancy: 9.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 42833 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPb

1gpb


Resolution: 2.1→126.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: NONE / ESU R: 0.201 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2263 2646 4.827 %
Rwork0.1685 --
all0.171 --
obs-54817 99.88 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.016 Å2-0 Å2-0 Å2
2---0.016 Å20 Å2
3---0.033 Å2
Refinement stepCycle: LAST / Resolution: 2.1→126.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6597 0 50 428 7075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136996
X-RAY DIFFRACTIONr_bond_other_d0.0350.0176498
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.659504
X-RAY DIFFRACTIONr_angle_other_deg2.2941.57815022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9095850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11521.463417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3741562
X-RAY DIFFRACTIONr_chiral_restr0.0780.2875
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.027932
X-RAY DIFFRACTIONr_gen_planes_other0.0220.021582
X-RAY DIFFRACTIONr_nbd_refined0.2080.21457
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.25938
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23305
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22961
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2367
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0130.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.214
X-RAY DIFFRACTIONr_nbd_other0.2350.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.214
X-RAY DIFFRACTIONr_mcbond_it3.0844.1123346
X-RAY DIFFRACTIONr_mcbond_other3.0844.1113345
X-RAY DIFFRACTIONr_mcangle_it4.1026.1464214
X-RAY DIFFRACTIONr_mcangle_other4.1016.1484215
X-RAY DIFFRACTIONr_scbond_it3.9774.5543650
X-RAY DIFFRACTIONr_scbond_other3.9764.5553651
X-RAY DIFFRACTIONr_scangle_it5.7796.6745290
X-RAY DIFFRACTIONr_scangle_other5.7796.6755291
X-RAY DIFFRACTIONr_lrange_it7.35647.9778005
X-RAY DIFFRACTIONr_lrange_other7.35647.9798006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.2761640.2443817X-RAY DIFFRACTION99.7994
2.154-2.2140.2561960.2123695X-RAY DIFFRACTION99.8973
2.214-2.2780.2471960.2183599X-RAY DIFFRACTION99.921
2.278-2.3480.2491970.1953487X-RAY DIFFRACTION100
2.348-2.4250.2651540.1833405X-RAY DIFFRACTION100
2.425-2.510.2261670.1663304X-RAY DIFFRACTION100
2.51-2.6040.2241760.1613175X-RAY DIFFRACTION100
2.604-2.7110.2411660.1663062X-RAY DIFFRACTION100
2.711-2.8310.2371540.1792946X-RAY DIFFRACTION99.9033
2.831-2.9690.2421580.1752794X-RAY DIFFRACTION99.9323
2.969-3.130.2591470.1762698X-RAY DIFFRACTION100
3.13-3.320.2161250.1712565X-RAY DIFFRACTION99.9628
3.32-3.5490.2691150.1782403X-RAY DIFFRACTION99.9603
3.549-3.8330.221090.1682257X-RAY DIFFRACTION100
3.833-4.1980.248880.1472099X-RAY DIFFRACTION99.8174
4.198-4.6930.163890.1291903X-RAY DIFFRACTION99.7496
4.693-5.4180.179720.1371694X-RAY DIFFRACTION99.774
5.418-6.6320.226810.1691445X-RAY DIFFRACTION99.8038
6.632-9.3670.201500.141145X-RAY DIFFRACTION99.6664
9.367-126.150.209420.216678X-RAY DIFFRACTION98.4952

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