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- PDB-1gpb: GLYCOGEN PHOSPHORYLASE B: DESCRIPTION OF THE PROTEIN STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1gpb
TitleGLYCOGEN PHOSPHORYLASE B: DESCRIPTION OF THE PROTEIN STRUCTURE
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
PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsJohnson, L.N. / Acharya, K.R. / Stuart, D.I.
Citation
Journal: Glycogen Phosphorylase B: Description of the Protein Structure
Year: 1991
Title: Glycogen Phosphorylase B: Description of the Protein Structure
Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N.
#1: 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.
#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
DepositionJun 4, 1990Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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

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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)97,5382
Polymers97,2911
Non-polymers2471
Water12,448691
1
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules

A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,0774
Polymers194,5822
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5780 Å2
ΔGint-21 kcal/mol
Surface area60610 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O
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 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.9 Å / σ(F): 3 /
RfactorNum. reflection
obs0.19 61344
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6691 0 15 691 7397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.025
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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