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- PDB-6gpb: REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPH... -

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Basic information

Entry
Database: PDB / ID: 6gpb
TitleREFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPHATE-OLIGOSACCHARIDE-AMP COMPLEX
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
alpha-maltopentaose / ADENOSINE MONOPHOSPHATE / Chem-H2P / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.86 Å
AuthorsAcharya, K.R. / Johnson, L.N.
Citation
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.
#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: 1991
Title: Structural Mechanism for Glycogen Phosphorylase Control by Phosphorylation and AMP
Authors: Barford, D. / Hu, S.-H. / Johnson, L.N.
#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 27, 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3366
Polymers97,2911
Non-polymers2,0445
Water10,953608
1
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules

A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,67112
Polymers194,5822
Non-polymers4,08910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10210 Å2
ΔGint-33 kcal/mol
Surface area60540 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

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-H2P / 1-deoxy-2-O-phosphono-alpha-D-gluco-hept-2-ulopyranose / HEPTULOSE-2-PHOSPHATE / 1-deoxy-2-O-phosphono-alpha-D-gluco-hept-2-ulose / 1-deoxy-2-O-phosphono-D-gluco-hept-2-ulose / 1-deoxy-2-O-phosphono-gluco-hept-2-ulose


Type: D-saccharide / Mass: 274.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H15O9P

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Non-polymers , 3 types, 611 molecules

#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: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN
Nonpolymer detailsMALTOHEPTAOSE CONSISTS OF SEVEN LINKED GLUCOSES. ONLY FIVE OF THE GLUCOSES WERE LOCATED IN THE ...MALTOHEPTAOSE CONSISTS OF SEVEN LINKED GLUCOSES. ONLY FIVE OF THE GLUCOSES WERE LOCATED IN THE ELECTRON DENSITY MAPS. THEY ARE PRESENTED AS GLUCOSES ON HETATM RECORDS BELOW.
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 ℃ / pH: 6.7 / Method: batch method / Details: took Mclaughlin et al., 1984 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlphosphorylase b11
22 mMIMP11
30.1 mMEDTA11

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Data collection

Reflection
*PLUS
Highest resolution: 2.86 Å / Num. obs: 18715 / Num. measured all: 88108 / Rmerge(I) obs: 0.063

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.86→8 Å
Details: THE N-TERMINAL RESIDUES 14 - 18 WERE ESTABLISHED TOWARDS THE END OF THE REFINEMENT. THESE RESIDUES ARE NOT WELL ORDERED. THEIR ATTACHMENT TO THE REST OF THE CHAIN CONTAINS SOME BAD ...Details: THE N-TERMINAL RESIDUES 14 - 18 WERE ESTABLISHED TOWARDS THE END OF THE REFINEMENT. THESE RESIDUES ARE NOT WELL ORDERED. THEIR ATTACHMENT TO THE REST OF THE CHAIN CONTAINS SOME BAD STEREOCHEMISTRY. A MORE CAREFUL AND CORRECT REPOSITIONING OF THESE RESIDUES IS GIVEN IN PROTEIN DATA BANK ENTRY 2GPB, THE T STATE PHOSPHORYLASE B COMPLEX WITH GLUCOSE.
RfactorNum. reflection
Rwork0.201 -
obs-19649
Refinement stepCycle: LAST / Resolution: 2.86→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 134 608 7469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg3.4
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
Refinement
*PLUS
Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.4

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