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- PDB-3syr: Glycogen phosphorylase b in complex with beta-D-glucopyranonucleo... -

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Basic information

Entry
Database: PDB / ID: 3syr
TitleGlycogen phosphorylase b in complex with beta-D-glucopyranonucleoside 5-fluorouracil
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / alpha and beta protein (a/b) / TRANSFERASE / muscle / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


SHG alpha-glucan phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / glycogen phosphorylase activity / glycogen phosphorylase / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Phosphorylase pyridoxal-phosphate attachment site / Glycogen/starch/alpha-glucan phosphorylase / Glycosyl transferase, family 35 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GPK / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsSkamnaki, V.T. / Kantsadi, A.L. / Kontou, M. / Leonidas, D.D.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: 3'-Axial CH(2) OH Substitution on Glucopyranose does not Increase Glycogen Phosphorylase Inhibitory Potency. QM/MM-PBSA Calculations Suggest Why.
Authors: Manta, S. / Xipnitou, A. / Kiritsis, C. / Kantsadi, A.L. / Hayes, J.M. / Skamnaki, V.T. / Lamprakis, C. / Kontou, M. / Zoumpoulakis, P. / Zographos, S.E. / Leonidas, D.D. / Komiotis, D.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)97,8122
Polymers97,5191
Non-polymers2921
Water3,711206
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6234
Polymers195,0392
Non-polymers5842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4240 Å2
ΔGint-21 kcal/mol
Surface area57880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.556, 128.556, 116.282
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 / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-GPK / 5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione


Type: D-saccharide / Mass: 292.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13FN2O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 2mM INHIBITOR SOAKED WITH T-STATE NATIVE ENZYME CRYSTAL FOR 2 HRS, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 2, 2011 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 36858 / Num. obs: 34960 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.11 / Net I/σ(I): 11.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2 / % possible all: 89.4

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Processing

Software
NameClassification
CrysalisProdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→13.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.749 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21718 1866 5.1 %RANDOM
Rwork0.17568 ---
all0.1778 36858 --
obs0.1778 34960 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→13.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6577 0 20 206 6803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226747
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9579136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81223.536345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.546151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6051559
X-RAY DIFFRACTIONr_chiral_restr0.110.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215167
X-RAY DIFFRACTIONr_mcbond_it0.6811.54019
X-RAY DIFFRACTIONr_mcangle_it1.34326490
X-RAY DIFFRACTIONr_scbond_it2.04632728
X-RAY DIFFRACTIONr_scangle_it3.5464.52646
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 120 -
Rwork0.226 2289 -
obs--88.02 %

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