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- PDB-2qll: Human liver glycogen phosphorylase- GL complex -

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Basic information

Entry
Database: PDB / ID: 2qll
TitleHuman liver glycogen phosphorylase- GL complex
Components
  • Glycogen phosphorylase, liver form
  • protein targeting to glycogen - GL
KeywordsTRANSFERASE / drug discovery / glycogen metabolism / protein-protein interaction / Allosteric enzyme / Carbohydrate metabolism / Disease mutation / Glycogen storage disease / Glycosyltransferase / Nucleotide-binding / Phosphorylation / Pyridoxal phosphate
Function / homology
Function and homology information


vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / AMP binding / necroptotic process / response to bacterium / pyridoxal phosphate binding / glucose homeostasis / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / 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 / Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.56 Å
AuthorsPautsch, A. / Streicher, R. / Wissdorf, O. / Stadler, N.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Molecular recognition of the protein phosphatase 1 glycogen targeting subunit by glycogen phosphorylase.
Authors: Pautsch, A. / Stadler, N. / Wissdorf, O. / Langkopf, E. / Moreth, W. / Streicher, R.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Mar 13, 2013Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, liver form
B: protein targeting to glycogen - GL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1023
Polymers97,8552
Non-polymers2471
Water2,774154
1
A: Glycogen phosphorylase, liver form
B: protein targeting to glycogen - GL
hetero molecules

A: Glycogen phosphorylase, liver form
B: protein targeting to glycogen - GL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,2046
Polymers195,7104
Non-polymers4942
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2215 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.986, 123.986, 125.695
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological assembly is generated by: Y,X,-Z+1

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Components

#1: Protein Glycogen phosphorylase, liver form /


Mass: 97356.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYGL / Cell (production host): High five cells / Production host: unidentified baculovirus / Strain (production host): SF9 / References: UniProt: P06737, glycogen phosphorylase
#2: Protein/peptide protein targeting to glycogen - GL


Mass: 498.529 Da / Num. of mol.: 1 / Fragment: GL-Cterm (281-284) / Source method: obtained synthetically / Details: peptide synthesis
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8 mg/ml protein, 0.1 M TRIS, 8% PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.56→19.5 Å / Num. obs: 37156 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 57.537 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.47
Reflection shellResolution: 2.56→2.71 Å / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 16543 / Num. unique all: 3929 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
BUSTER-TNT2.1.1refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.56→19.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1769 5 %RANDOM
Rwork0.203 ---
obs0.206 37156 97.36 %-
Displacement parametersBiso mean: 65.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.808 Å20 Å20 Å2
2---1.808 Å20 Å2
3---3.616 Å2
Refinement stepCycle: LAST / Resolution: 2.56→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6565 0 15 154 6734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg1.12
LS refinement shellResolution: 2.56→2.71 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.462 264 5 %
Rwork0.4 5021 -
obs-5285 97.36 %

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