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- PDB-3bd6: Glycogen Phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid -

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Basic information

Entry
Database: PDB / ID: 3bd6
TitleGlycogen Phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphorylation / Pyridoxal phosphate
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-RDD / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSovantzis, D.A. / Hadjiloi, T. / Hayes, J.M. / Zographos, S.E. / Chrysina, E.D. / Oikonomakos, N.G.
CitationJournal: To be Published
Title: D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b
Authors: Cisma, C. / Sovantzis, D.A. / Hadjiloi, T. / Stathis, D. / Gimisis, T. / Hayes, J.M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Oikonomakos, N.G.
History
DepositionNov 14, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)97,7812
Polymers97,5191
Non-polymers2611
Water4,738263
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5614
Polymers195,0392
Non-polymers5222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4580 Å2
ΔGint-23.1 kcal/mol
Surface area57180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.620, 128.620, 116.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-RDD / 1-beta-D-ribofuranosyl-1,3,5-triazinane-2,4,6-trione


Mass: 261.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N3O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 50.16 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10mM Bes buffer, 3mM DDT, pH6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 2, 2005
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 65282 / Num. obs: 65282 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.047 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.435 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2PRJ

2prj


Resolution: 2→21.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.444 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20515 3311 5.1 %RANDOM
Rwork0.19015 ---
obs0.19092 61937 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.177 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.85 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2→21.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 18 263 6919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226807
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9569214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0255810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95923.486350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.174151185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5311560
X-RAY DIFFRACTIONr_chiral_restr0.0740.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025221
X-RAY DIFFRACTIONr_nbd_refined0.180.22817
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2347
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.26
X-RAY DIFFRACTIONr_mcbond_it0.5471.54191
X-RAY DIFFRACTIONr_mcangle_it0.94126534
X-RAY DIFFRACTIONr_scbond_it1.20533011
X-RAY DIFFRACTIONr_scangle_it1.9694.52680
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 257 -
Rwork0.237 4450 -
obs--97.98 %

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