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- PDB-2f3u: Crystal Structure of the glycogen phosphorylase B / N-(beta-D-glu... -

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Basic information

Entry
Database: PDB / ID: 2f3u
TitleCrystal Structure of the glycogen phosphorylase B / N-(beta-D-glucopyranosyl)-N'-cyclopropyl oxalamide complex
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes
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
Chem-8GP / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.93 Å
AuthorsOikonomakos, N.G. / Leonidas, D.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2006
Title: Binding of oxalyl derivatives of beta-d-glucopyranosylamine to muscle glycogen phosphorylase b.
Authors: Hadjiloi, T. / Tiraidis, C. / Chrysina, E.D. / Leonidas, D.D. / Oikonomakos, N.G. / Tsipos, P. / Gimisis, T.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 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, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8293
Polymers97,2911
Non-polymers5372
Water5,405300
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6576
Polymers194,5822
Non-polymers1,0754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6930 Å2
ΔGint-9 kcal/mol
Surface area55840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.957, 127.957, 116.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimeric glycogen phosphorylase is the physiologically active species

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


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: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Sugar ChemComp-8GP / N-[(cyclopropylamino)(oxo)acetyl]-beta-D-glucopyranosylamine / N-(BETA-D-GLUCOPYRANOSYL)-N'-CYCLOPROPYL OXALAMIDE / N-[(cyclopropylamino)(oxo)acetyl]-beta-D-glucosylamine / N-[(cyclopropylamino)(oxo)acetyl]-D-glucosylamine / N-[(cyclopropylamino)(oxo)acetyl]-glucosylamine


Type: D-saccharide / Mass: 290.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N2O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8034 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2005
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8034 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. all: 72265 / Num. obs: 72265 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 6.6
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3554 / Rsym value: 0.38 / % possible all: 99.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2PRJ

2prj


Resolution: 1.93→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2105 3668 RANDOM
Rwork0.1908 --
all0.2 72158 -
obs0.2 72158 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.487 Å20 Å20 Å2
2---3.487 Å20 Å2
3---6.973 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.93→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 35 300 6924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 1.93→2 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.2646 385 -
Rwork0.2607 --
obs-7097 99.1 %

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