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- PDB-3bcr: Glycogen Phosphorylase b in complex with AZT -

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Basic information

Entry
Database: PDB / ID: 3bcr
TitleGlycogen Phosphorylase b in complex with AZT
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphorylation / Pyridoxal phosphate
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
3'-azido-3'-deoxythymidine / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.14 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 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2012Group: Non-polymer description

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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)97,7872
Polymers97,5191
Non-polymers2671
Water4,900272
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5734
Polymers195,0392
Non-polymers5342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4500 Å2
ΔGint-22.6 kcal/mol
Surface area57090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.436, 128.436, 116.310
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: Chemical ChemComp-AZZ / 3'-azido-3'-deoxythymidine / Azidothymidine / Zidovudine / Zidovudine


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Comment: medication, antiretroviral*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 49.98 %
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: X13 / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2007
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.14→30 Å / Num. all: 53628 / Num. obs: 53628 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.036 / Net I/σ(I): 17.2
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.497 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PRJ
Resolution: 2.14→24.73 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.553 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21882 2723 5.1 %RANDOM
Rwork0.1834 ---
obs0.18516 50869 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.776 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.84 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.14→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 19 272 6919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226808
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.9569214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1485810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36723.486350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42151185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6231560
X-RAY DIFFRACTIONr_chiral_restr0.0760.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025221
X-RAY DIFFRACTIONr_nbd_refined0.1820.22885
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2364
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.24
X-RAY DIFFRACTIONr_mcbond_it0.5551.54176
X-RAY DIFFRACTIONr_mcangle_it0.97226534
X-RAY DIFFRACTIONr_scbond_it1.24533011
X-RAY DIFFRACTIONr_scangle_it2.074.52680
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 191 -
Rwork0.228 3680 -
obs--98.4 %

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