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- PDB-5o50: Glycogen Phosphorylase b in complex with 33a -

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Basic information

Entry
Database: PDB / ID: 5o50
TitleGlycogen Phosphorylase b in complex with 33a
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / alpha and beta protein
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
Chem-9L2 / INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsKantsadi, A.L. / Kyriakis, E. / Stravodimos, G.A. / Solovou, T.G.A. / Chatzileontiadou, D.S. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Nanomolar Inhibitors of Glycogen Phosphorylase Based on beta-d-Glucosaminyl Heterocycles: A Combined Synthetic, Enzyme Kinetic, and Protein Crystallography Study.
Authors: Bokor, E. / Kyriakis, E. / Solovou, T.G.A. / Koppany, C. / Kantsadi, A.L. / Szabo, K.E. / Szakacs, A. / Stravodimos, G.A. / Docsa, T. / Skamnaki, V.T. / Zographos, S.E. / Gergely, P. / ...Authors: Bokor, E. / Kyriakis, E. / Solovou, T.G.A. / Koppany, C. / Kantsadi, A.L. / Szabo, K.E. / Szakacs, A. / Stravodimos, G.A. / Docsa, T. / Skamnaki, V.T. / Zographos, S.E. / Gergely, P. / Leonidas, D.D. / Somsak, L.
History
DepositionMay 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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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)98,1924
Polymers97,2911
Non-polymers9013
Water5,783321
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3848
Polymers194,5822
Non-polymers1,8016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7000 Å2
ΔGint-30 kcal/mol
Surface area57140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.480, 128.480, 116.260
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: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-9L2 / (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-phenyl-1~{H}-imidazol-2-yl)oxane-3,4-diol


Mass: 305.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N3O4
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H13N4O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 50.12 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10 mM BES buffer

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.9→40.86 Å / Num. obs: 76499 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rsym value: 0.073 / Net I/σ(I): 12
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 10969 / Rsym value: 0.468 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→40.86 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.844 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16098 3840 5 %RANDOM
Rwork0.13044 ---
obs0.13197 72620 99.42 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 33.917 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å2-0 Å2
2--0.46 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 1.9→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 60 321 6971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196834
X-RAY DIFFRACTIONr_bond_other_d0.0010.026321
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9619265
X-RAY DIFFRACTIONr_angle_other_deg0.943314610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7875817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02723.514350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.799151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6441560
X-RAY DIFFRACTIONr_chiral_restr0.0830.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021474
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_it2.5861.7943247
X-RAY DIFFRACTIONr_mcbond_other2.5741.7933246
X-RAY DIFFRACTIONr_mcangle_it3.6672.6694056
X-RAY DIFFRACTIONr_mcangle_other3.6692.6714057
X-RAY DIFFRACTIONr_scbond_it4.6212.4563587
X-RAY DIFFRACTIONr_scbond_other4.6222.4533583
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9793.4435199
X-RAY DIFFRACTIONr_long_range_B_refined8.52221.727548
X-RAY DIFFRACTIONr_long_range_B_other8.52221.7267549
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 266 -
Rwork0.219 5297 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 28.272 Å / Origin y: 21.33 Å / Origin z: 31.61 Å
111213212223313233
T0.0421 Å2-0.042 Å20.0057 Å2-0.0912 Å2-0.0279 Å2--0.0172 Å2
L0.5928 °20.0611 °2-0.0345 °2-0.4977 °2-0.1295 °2--0.9133 °2
S-0.0373 Å °0.0531 Å °0.0461 Å °-0.0232 Å °0.0038 Å °0.0198 Å °0.075 Å °-0.1053 Å °0.0336 Å °

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