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- PDB-5jtu: Crystal structure of GPb in complex with 8b -

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Basic information

Entry
Database: PDB / ID: 5jtu
TitleCrystal structure of GPb in complex with 8b
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / alpha and beta protein transferase
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-6NE / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsKantsadi, A.L. / Stravodimos, G.A. / Chatzileontiadou, D.S.M. / Leonidas, D.D.
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Synthetic, enzyme kinetic, and protein crystallographic studies of C-beta-d-glucopyranosyl pyrroles and imidazoles reveal and explain low nanomolar inhibition of human liver glycogen phosphorylase.
Authors: Kantsadi, A.L. / Bokor, E. / Kun, S. / Stravodimos, G.A. / Chatzileontiadou, D.S. / Leonidas, D.D. / Juhasz-Toth, E. / Szakacs, A. / Batta, G. / Docsa, T. / Gergely, P. / Somsak, L.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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)98,1825
Polymers97,4221
Non-polymers7604
Water5,837324
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,36410
Polymers194,8452
Non-polymers1,5208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5520 Å2
ΔGint-12 kcal/mol
Surface area56800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.620, 128.620, 116.290
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: 97422.398 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-6NE / (1S)-1,5-anhydro-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]-D-glucitol


Mass: 356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O5
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10mM BES buffer

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0403 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 6, 2015
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0403 Å / Relative weight: 1
ReflectionResolution: 1.85→38.76 Å / Num. obs: 74394 / % possible obs: 89.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 4.9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.6 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→38.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.659 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20269 3638 4.9 %RANDOM
Rwork0.17025 ---
obs0.17186 70718 89.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.987 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.56 Å2
Refinement stepCycle: 1 / Resolution: 1.85→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 49 324 6962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196797
X-RAY DIFFRACTIONr_bond_other_d0.0010.026496
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9599204
X-RAY DIFFRACTIONr_angle_other_deg0.79314870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37623.534348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.319151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7451559
X-RAY DIFFRACTIONr_chiral_restr0.0820.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021658
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 311 -
Rwork0.24 5429 -
obs--94.21 %

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