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- PDB-5ikp: Crystal structure of human brain glycogen phosphorylase bound to AMP -

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Basic information

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


maltodextrin phosphorylase activity / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / azurophil granule lumen / pyridoxal phosphate binding / Neutrophil degranulation / extracellular exosome / extracellular region ...maltodextrin phosphorylase activity / glycogen phosphorylase / glycogen 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
ADENOSINE MONOPHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, brain form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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)97,7053
Polymers97,1101
Non-polymers5942
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-6 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.040, 172.040, 123.590
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) / Gene: PYGB / Production host: Escherichia coli (E. coli) / References: UniProt: P11216, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 2.71 Å3/Da / Density % sol: 54.63 %
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: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 3.4→47.56 Å / Num. obs: 15352 / % possible obs: 99.7 % / Redundancy: 19 % / Net I/σ(I): 27.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z8D

1z8d


Resolution: 3.4→47.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.897 / SU B: 37.541 / SU ML: 0.559 / Cross valid method: THROUGHOUT / ESU R Free: 0.685 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2951 768 5 %RANDOM
Rwork0.20245 ---
obs0.20709 14583 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 119.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å2-0 Å2
3----1.11 Å2
Refinement stepCycle: 1 / Resolution: 3.4→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 23 0 6558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196710
X-RAY DIFFRACTIONr_bond_other_d0.0030.026406
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9629090
X-RAY DIFFRACTIONr_angle_other_deg1.135314716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7885802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.06423.927331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.35151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8141548
X-RAY DIFFRACTIONr_chiral_restr0.0860.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217541
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_it6.26611.673220
X-RAY DIFFRACTIONr_mcbond_other6.25511.6683219
X-RAY DIFFRACTIONr_mcangle_it9.65717.54018
X-RAY DIFFRACTIONr_mcangle_other9.65617.5034019
X-RAY DIFFRACTIONr_scbond_it5.9512.183490
X-RAY DIFFRACTIONr_scbond_other5.94912.183491
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.58718.0755073
X-RAY DIFFRACTIONr_long_range_B_refined14.84728702
X-RAY DIFFRACTIONr_long_range_B_other14.84728703
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.399→3.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 54 -
Rwork0.291 1020 -
obs--97.37 %

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