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- PDB-2pri: BINDING OF 2-DEOXY-GLUCOSE-6-PHOSPHATE TO GLYCOGEN PHOSPHORYLASE B -

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Basic information

Entry
Database: PDB / ID: 2pri
TitleBINDING OF 2-DEOXY-GLUCOSE-6-PHOSPHATE TO GLYCOGEN PHOSPHORYLASE B
ComponentsGLYCOGEN PHOSPHORYLASE B
KeywordsTRANSFERASE / GLYCOGEN 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
2-deoxy-6-O-phosphono-alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOikonomakos, N.G. / Zographos, S.E. / Johnson, L.N. / Papageorgiou, A.C. / Acharya, K.R.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies.
Authors: Oikonomakos, N.G. / Zographos, S.E. / Johnson, L.N. / Papageorgiou, A.C. / Acharya, K.R.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallographic Binding Studies on the Allosteric Inhibitor Glucose-6- Phosphate to T State Glycogen Phosphorylase B
Authors: Johnson, L.N. / Snape, P. / Martin, J.L. / Acharya, K.R. / Barford, D. / Oikonomakos, N.G.
History
DepositionDec 11, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 14, 1998Provider: repository / Type: Initial release
SupersessionDec 16, 1998ID: 1PRI
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 29, 2012Group: Non-polymer description
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 30, 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 B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7823
Polymers97,2911
Non-polymers4912
Water4,594255
1
A: GLYCOGEN PHOSPHORYLASE B
hetero molecules

A: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5656
Polymers194,5822
Non-polymers9834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7380 Å2
ΔGint-32 kcal/mol
Surface area58600 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
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein GLYCOGEN PHOSPHORYLASE B / E.C.2.4.1.1


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-D6G / 2-deoxy-6-O-phosphono-alpha-D-glucopyranose / 2-deoxy-6-O-phosphono-alpha-D-arabino-hexopyranose / 2-deoxy-alpha-D-glucopyranose 6-phosphate / 2-deoxy-6-O-phosphono-alpha-D-glucose / 2-deoxy-6-O-phosphono-D-glucose / 2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 244.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O8P
IdentifierTypeProgram
a-D-2-deoxy-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / 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: 2.47 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: THE PROTEIN WAS CRYSTALLISED FROM 10 MM BES, PH 6.7, 3 MM DITHIOTHREITOL, 0.1 MM EDTA, 0.02% SODIUM AZIDE. THE CRYSTALS WERE THEN SOAKED FOR ONE HOUR IN 100 MM 2-DEOXY-D-GLUCOSE-6-PHOSPHATE. ...Details: THE PROTEIN WAS CRYSTALLISED FROM 10 MM BES, PH 6.7, 3 MM DITHIOTHREITOL, 0.1 MM EDTA, 0.02% SODIUM AZIDE. THE CRYSTALS WERE THEN SOAKED FOR ONE HOUR IN 100 MM 2-DEOXY-D-GLUCOSE-6-PHOSPHATE., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1DITHIOTHREITOL11
2BES11
3EDTA11
4NAN311
Crystal grow
*PLUS
Details: Oikonomakos, N.G., (1985) Biochim. Biophys. Acta, 832, 248.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Date: Aug 26, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.17 Å / Num. obs: 41448 / % possible obs: 94.7 % / Redundancy: 1.82 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.4 Å / % possible all: 76.8
Reflection
*PLUS
Num. measured all: 75440

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PRJ

2prj


Resolution: 2.3→28.17 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 --RANDOM
Rwork0.192 ---
obs0.192 41448 94.7 %-
all-41448 --
Refinement stepCycle: LAST / Resolution: 2.3→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 30 255 7034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
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 / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 40308 / σ(F): 0 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

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