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- PDB-1fa9: HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH AMP -

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Basic information

Entry
Database: PDB / ID: 1fa9
TitleHUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH AMP
ComponentsGLYCOGEN PHOSPHORYLASE, LIVER FORM
KeywordsTRANSFERASE / protein-ligand complex / allosteric protein / phosphorylated protein
Function / homology
Function and homology information


vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / : / : / bile acid binding / glycogen catabolic process ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / 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 / 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
ADENOSINE MONOPHOSPHATE / alpha-D-glucopyranose / 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.N. / 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 12, 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: Derived calculations / 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 / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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 / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE, LIVER FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0004
Polymers97,2251
Non-polymers7753
Water4,360242
1
A: GLYCOGEN PHOSPHORYLASE, LIVER FORM
hetero molecules

A: GLYCOGEN PHOSPHORYLASE, LIVER FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,0008
Polymers194,4512
Non-polymers1,5496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area10080 Å2
ΔGint-30 kcal/mol
Surface area61620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.91, 123.91, 127.68
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein GLYCOGEN PHOSPHORYLASE, LIVER FORM


Mass: 97225.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Plasmid: PKK2332 / Production host: Escherichia coli (E. coli) / References: UniProt: P06737, glycogen phosphorylase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Peg 8000, Tris/HCl, AMP, glucose, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal grow
*PLUS
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
220 mMNaBES1drop
31 mMEDTA1drop
40.5 mMdithiothreitol1drop
550 mMglucose1drop
60.1 MTris-HCl1reservoir
712 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 19, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 44772 / Num. obs: 43732 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 9 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.495 / % possible all: 91.8
Reflection
*PLUS
Num. obs: 53400
Reflection shell
*PLUS
% possible obs: 91.8 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPA

1gpa


Resolution: 2.4→50 Å / Cross valid method: X-PLOR / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 4101 10 %random
Rwork0.235 ---
all0.221 43732 --
obs0.221 43732 --
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 50 242 7042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.4→2.42 Å / Rfactor Rfree: 0.476 / Rfactor Rwork: 0.353
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Rfactor Rfree: 0.476 / Rfactor Rwork: 0.353 / Rfactor obs: 0.353

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