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- PDB-5o52: Glycogen Phosphorylase b in complex with 33b -

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Basic information

Entry
Database: PDB / ID: 5o52
TitleGlycogen Phosphorylase b in complex with 33b
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. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9LE / 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)98,3804
Polymers97,4221
Non-polymers9583
Water5,477304
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,7618
Polymers194,8452
Non-polymers1,9166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5980 Å2
ΔGint-23 kcal/mol
Surface area57010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.730, 128.730, 116.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1301-

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) / 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-9LE / (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-naphthalen-2-yl-1~{H}-imidazol-2-yl)oxane-3,4-diol


Mass: 355.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 50.24 %
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→38.42 Å / Num. obs: 75575 / % possible obs: 98.4 % / Redundancy: 4 % / Rsym value: 0.073 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 10839 / Rsym value: 0.45 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→38.42 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 4.94 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15778 3792 5 %RANDOM
Rwork0.13075 ---
obs0.1321 71740 97.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 32.447 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-0 Å2
2--0.39 Å20 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 67 304 6961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196837
X-RAY DIFFRACTIONr_bond_other_d0.0010.026329
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9639267
X-RAY DIFFRACTIONr_angle_other_deg0.946314622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47423.524349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.885151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591560
X-RAY DIFFRACTIONr_chiral_restr0.0830.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021480
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_it2.4291.6613248
X-RAY DIFFRACTIONr_mcbond_other2.4251.6593247
X-RAY DIFFRACTIONr_mcangle_it3.4472.4714058
X-RAY DIFFRACTIONr_mcangle_other3.452.4734059
X-RAY DIFFRACTIONr_scbond_it4.5512.3083588
X-RAY DIFFRACTIONr_scbond_other4.5512.3083589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8953.2315206
X-RAY DIFFRACTIONr_long_range_B_refined8.420.3717571
X-RAY DIFFRACTIONr_long_range_B_other8.39920.3727572
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
Rfree0.231 264 -
Rwork0.212 5227 -
obs--97.27 %
Refinement TLS params.Method: refined / Origin x: 28.332 Å / Origin y: 21.303 Å / Origin z: 31.605 Å
111213212223313233
T0.0513 Å2-0.0408 Å20.0048 Å2-0.0958 Å2-0.0266 Å2--0.0135 Å2
L0.5683 °20.0834 °2-0.0527 °2-0.4839 °2-0.1355 °2--0.8761 °2
S-0.0346 Å °0.0562 Å °0.0362 Å °-0.0231 Å °0.0053 Å °0.014 Å °0.071 Å °-0.09 Å °0.0293 Å °

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