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- PDB-5iko: Crystal structure of human brain glycogen phosphorylase -

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Basic information

Entry
Database: PDB / ID: 5iko
TitleCrystal structure of human brain glycogen phosphorylase
ComponentsGlycogen phosphorylase, brain form
KeywordsTRANSFERASE / GP / GLYCOGEN PHOSPHORYLASE / GLYCOGEN METABOLISM / GLYCOGEN DISEASE / GLYCOSYLTRANSFERASE / NUCLEOTIDE-BINDING / ALLOSTERIC ENZYME
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / azurophil granule lumen / pyridoxal phosphate binding / Neutrophil degranulation / extracellular exosome ...glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / azurophil granule lumen / pyridoxal phosphate binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / cytoplasm
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
PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Glycogen phosphorylase, brain form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMathieu, C. / Li de la Sierra-Gallay, I. / Xu, X. / Haouz, A. / Rodrigues-Lima, F.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Insights into Brain Glycogen Metabolism: THE STRUCTURE OF HUMAN BRAIN GLYCOGEN PHOSPHORYLASE.
Authors: Mathieu, C. / de la Sierra-Gallay, I.L. / Duval, R. / Xu, X. / Cocaign, A. / Leger, T. / Woffendin, G. / Camadro, J.M. / Etchebest, C. / Haouz, A. / Dupret, J.M. / Rodrigues-Lima, F.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Glycogen phosphorylase, brain form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1126
Polymers97,1101
Non-polymers1,0025
Water1,51384
1
A: Glycogen phosphorylase, brain form
hetero molecules

A: Glycogen phosphorylase, brain form
hetero molecules

A: Glycogen phosphorylase, brain form
hetero molecules

A: Glycogen phosphorylase, brain form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,44824
Polymers388,4414
Non-polymers4,00720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_785-x+2,-y+3,z1
crystal symmetry operation9_767-x+2,-x+y+1,-z+21
crystal symmetry operation12_577x,x-y+2,-z+21
Buried area21180 Å2
ΔGint-74 kcal/mol
Surface area115310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.660, 171.660, 122.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Glycogen phosphorylase, brain form /


Mass: 97110.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BRAIN ISOFORM / Gene: PYGB / Production host: Escherichia coli (E. coli) / References: UniProt: P11216, glycogen phosphorylase
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P / References: glycogen phosphorylase
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28 % (v/v) PEG 400, 0.2 M calcium chloride, and 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.5→47.37 Å / Num. obs: 37317 / % possible obs: 99.2 % / Redundancy: 26 % / Net I/σ(I): 20.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z8D
Resolution: 2.5→47.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.873 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.264 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23855 1866 5 %RANDOM
Rwork0.18651 ---
obs0.18916 35450 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å2-0 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 48 84 6672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196743
X-RAY DIFFRACTIONr_bond_other_d0.0020.026458
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9639119
X-RAY DIFFRACTIONr_angle_other_deg1.087314842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5695805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37123.916332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.259151166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5251548
X-RAY DIFFRACTIONr_chiral_restr0.1020.2986
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021579
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_it5.1656.5873226
X-RAY DIFFRACTIONr_mcbond_other5.1646.5863225
X-RAY DIFFRACTIONr_mcangle_it7.0539.8864026
X-RAY DIFFRACTIONr_mcangle_other7.0539.8884027
X-RAY DIFFRACTIONr_scbond_it6.0937.1793515
X-RAY DIFFRACTIONr_scbond_other6.0927.1793515
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.68710.5335093
X-RAY DIFFRACTIONr_long_range_B_refined11.36163.08428583
X-RAY DIFFRACTIONr_long_range_B_other11.36263.08628573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 131 -
Rwork0.289 2499 -
obs--96.73 %

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