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- PDB-1fc0: HUMAN LIVER GLYCOGEN PHOSPHORYLASE COMPLEXED WITH N-ACETYL-BETA-D... -

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Basic information

Entry
Database: PDB / ID: 1fc0
TitleHUMAN LIVER GLYCOGEN PHOSPHORYLASE COMPLEXED WITH N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE
ComponentsGLYCOGEN PHOSPHORYLASE, LIVER FORM
KeywordsTRANSFERASE / phosphorylated protein / allosteric / glucose analog / inhibitor
Function / homology
Function and homology information


purine nucleobase binding / vitamin binding / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / bile acid binding / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / AMP binding ...purine nucleobase binding / vitamin binding / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / bile acid binding / glycogen catabolic process / 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 / cytoplasm / cytosol
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
N-acetyl-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRath, V.L. / Ammirati, M. / LeMotte, P.K. / Fennell, K.F. / Mansour, M.M. / Danley, D.E. / Hynes, T.R. / Schulte, G.K. / Wasilko, D.J. / Pandit, J.
CitationJournal: Mol.Cell / Year: 2000
Title: Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core.
Authors: Rath, V.L. / Ammirati, M. / LeMotte, P.K. / Fennell, K.F. / Mansour, M.N. / Danley, D.E. / Hynes, T.R. / Schulte, G.K. / Wasilko, D.J. / Pandit, J.
History
DepositionJul 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE, LIVER FORM
B: GLYCOGEN PHOSPHORYLASE, LIVER FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,2276
Polymers194,2912
Non-polymers9374
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-9 kcal/mol
Surface area56140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.000, 124.000, 122.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsThe biological assembly is a dimer related by a two fold NCS axis. Monomer 1 consists of residues A23-A831, monomer 2 consists of residues A1023-A1831.

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Components

#1: Protein GLYCOGEN PHOSPHORYLASE, LIVER FORM


Mass: 97145.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Plasmid: PBLUEBAC III / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06737, glycogen phosphorylase
#2: Sugar ChemComp-NBG / N-acetyl-beta-D-glucopyranosylamine / 1-N-ACETYL-BETA-D-GLUCOSAMINE / N-acetyl-beta-D-glucosylamine / N-acetyl-D-glucosylamine / N-acetyl-glucosylamine


Type: D-saccharide / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
b-D-Glcp1NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: NaMES, MPD, N-acetyl-beta-D-glycopyranosylamine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 17K
Crystal grow
*PLUS
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-40 mg/mlprotein1drop
220 mMNaBES1drop
31 mMEDTA1drop
40.5 mMdithiothreitol1drop
530-80 mMN-acetyl-beta-D-glucopyranosylamine1drop
60.1 Msodium MES1reservoir
725-35 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 82210 / Num. obs: 81720 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.3 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 22.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.174 / % possible all: 97.8
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FA9

1fa9


Resolution: 2.4→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 549432.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.235 7804 10 %RANDOM
Rwork0.198 ---
obs0.198 78076 95.1 %-
all-81964 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.63 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20.99 Å20 Å2
2---2.72 Å20 Å2
3---5.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12854 0 60 255 13169
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.52
X-RAY DIFFRACTIONc_mcbond_it2.581.5
X-RAY DIFFRACTIONc_mcangle_it3.952
X-RAY DIFFRACTIONc_scbond_it4.022
X-RAY DIFFRACTIONc_scangle_it5.782.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 1183 10.1 %
Rwork0.268 10520 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLPPHO.PARAMPLPPHO_PATCH.TOP
X-RAY DIFFRACTION4GNC.PARAMGNC.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.52
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.283 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.268

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