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- PDB-8gpb: STRUCTURAL MECHANISM FOR GLYCOGEN PHOSPHORYLASE CONTROL BY PHOSPH... -

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Basic information

Entry
Database: PDB / ID: 8gpb
TitleSTRUCTURAL MECHANISM FOR GLYCOGEN PHOSPHORYLASE CONTROL BY PHOSPHORYLATION AND AMP
ComponentsGLYCOGEN PHOSPHORYLASE B
KeywordsGLYCOGEN PHOSPHORYLASE
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
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, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsBarford, D. / Hu, S.-H. / Johnson, L.N.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP.
Authors: Barford, D. / Hu, S.H. / Johnson, L.N.
#1: Journal: Glycogen Phosphorylase B: Description of the Protein Structure
Title: Glycogen Phosphorylase B: Description of the Protein Structure 1 1991
Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Refined Crystal Structure of the Phosphorylase-Heptulose 2-Phosphate-Oligosaccharide-AMP Complex
Authors: Johnson, L.N. / Acharya, K.R. / Jordan, M.D. / Mclaughlin, P.J.
#3: Journal: Biochemistry / Year: 1990
Title: Comparison of the Binding of Glucose and Glucose-1-Phosphate Derivatives to T-State Glycogen Phosphorylase B
Authors: Martin, J.L. / Johnson, L.N. / Withers, S.G.
#4: Journal: Nature / Year: 1989
Title: The Allosteric Transition of Glycogen Phosphorylase
Authors: Barford, D. / Johnson, L.N.
#5: Journal: Nature / Year: 1988
Title: Structural Changes in Glycogen Phosphorylase Induced by Phosphorylation
Authors: Sprang, S.R. / Acharya, K.R. / Goldsmith, E.J. / Stuart, D.I. / Varvill, K. / Fletterick, R.J. / Madsen, N.B. / Johnson, L.N.
History
DepositionNov 13, 1990Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2334
Polymers97,2911
Non-polymers9423
Water11,530640
1
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules

A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,4668
Polymers194,5822
Non-polymers1,8836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7880 Å2
ΔGint-29 kcal/mol
Surface area59960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.500, 128.500, 116.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986) BUT IT HAS BEEN PRESENTED AS ILE IN THIS ENTRY. THIS ASSIGNMENT WAS MADE IN THE ORIGINAL ...1: RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986) BUT IT HAS BEEN PRESENTED AS ILE IN THIS ENTRY. THIS ASSIGNMENT WAS MADE IN THE ORIGINAL STRUCTURE DETERMINATION AT 1.9 ANGSTROMS (PRESENTED IN PROTEIN DATA BANK ENTRY 1GPB) AND CARRIED THROUGH TO THE OTHER ENTRIES. ILE IS MORE CONSISTENT WITH THE ELECTRON DENSITY. HOWEVER, THE RESOLUTION AT 1.9 ANGSTROMS DOES NOT ALLOW A DEFINITIVE ASSIGNMENT.

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Components

#1: Protein GLYCOGEN PHOSPHORYLASE B


Mass: 97291.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsRESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, ...RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986) BUT IT HAS BEEN PRESENTED AS ILE IN THIS ENTRY. THIS ASSIGNMENT WAS MADE IN THE ORIGINAL STRUCTURE DETERMINATION AT 1.9 ANGSTROMS (PRESENTED IN PROTEIN DATA BANK ENTRY 1GPB) AND CARRIED THROUGH TO THE OTHER ENTRIES. ILE IS MORE CONSISTENT WITH THE ELECTRON DENSITY. HOWEVER, THE RESOLUTION AT 1.9 ANGSTROMS DOES NOT ALLOW A DEFINITIVE ASSIGNMENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: batch method / Details: took Johnson et al., 1974 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3 Mdithiothreitol11
21 Mmagnesium acetate11
30.2 MIMP11
40.2 mM11NaF
50.03 %sodium azide11

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 36295 / % possible obs: 80 % / Num. measured all: 165007 / Rmerge(I) obs: 0.08

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.206 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6761 0 61 640 7462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 36167 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.6

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