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- PDB-4mra: Crystal structure of Gpb in complex with QUERCETIN -

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Basic information

Entry
Database: PDB / ID: 4mra
TitleCrystal structure of Gpb in complex with QUERCETIN
ComponentsGlycogen phosphorylase, muscle form
KeywordsTransferase/transferase inhibitor / alpha and beta protein / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


glycogen phosphorylase / glycogen 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. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,5,7,3',4'-PENTAHYDROXYFLAVONE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.34 Å
AuthorsKantsadi, L.A. / Chatzileontiadou, S.M.D. / Leonidas, D.D.
CitationJournal: Food Chem.Toxicol. / Year: 2014
Title: Biochemical and biological assessment of the inhibitory potency of extracts from vinification byproducts of Vitis vinifera extracts against glycogen phosphorylase.
Authors: Kantsadi, A.L. / Apostolou, A. / Theofanous, S. / Stravodimos, G.A. / Kyriakis, E. / Gorgogietas, V.A. / Chatzileontiadou, D.S. / Pegiou, K. / Skamnaki, V.T. / Stagos, D. / Kouretas, D. / ...Authors: Kantsadi, A.L. / Apostolou, A. / Theofanous, S. / Stravodimos, G.A. / Kyriakis, E. / Gorgogietas, V.A. / Chatzileontiadou, D.S. / Pegiou, K. / Skamnaki, V.T. / Stagos, D. / Kouretas, D. / Psarra, A.M. / Haroutounian, S.A. / Leonidas, D.D.
History
DepositionSep 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8893
Polymers95,5091
Non-polymers3802
Water6,341352
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,7796
Polymers191,0182
Non-polymers7614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5930 Å2
ΔGint-26 kcal/mol
Surface area56470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.600, 126.600, 115.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 95509.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 23, 2013
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.34→30 Å / Num. all: 40399 / Num. obs: 40399 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rsym value: 0.101 / Net I/σ(I): 18
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 10 % / Mean I/σ(I) obs: 5 / Rsym value: 0.461 / % possible all: 100

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Processing

Software
NameClassification
DNAdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3SYM

3sym


Resolution: 2.34→29.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.084 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24395 2023 5 %RANDOM
Rwork0.17866 ---
obs0.18196 38265 99.65 %-
all-38265 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.332 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.34→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 26 352 6956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196761
X-RAY DIFFRACTIONr_bond_other_d0.0010.026458
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9599156
X-RAY DIFFRACTIONr_angle_other_deg0.895314783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39123.497346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.341151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9551560
X-RAY DIFFRACTIONr_chiral_restr0.1020.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021645
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1882.8133227
X-RAY DIFFRACTIONr_mcbond_other2.1842.8113226
X-RAY DIFFRACTIONr_mcangle_it3.3934.2014029
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.853.1963534
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.337→2.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 147 -
Rwork0.203 2736 -
obs--98.06 %

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