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- PDB-1axr: COOPERATIVITY BETWEEN HYDROGEN-BONDING AND CHARGE-DIPOLE INTERACT... -

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Basic information

Entry
Database: PDB / ID: 1axr
TitleCOOPERATIVITY BETWEEN HYDROGEN-BONDING AND CHARGE-DIPOLE INTERACTIONS IN THE INHIBITION OF BETA-GLYCOSIDASES BY AZOLOPYRIDINES: EVIDENCE FROM A STUDY WITH GLYCOGEN PHOSPHORYLASE B
ComponentsGLYCOGEN PHOSPHORYLASE
KeywordsTRANSFERASE / GLYCOSIDASES / GLYCOGEN PHOSPHORYLASE / CATALYTIC MECHANISM / AZOLOPYRIDINES / INHIBITORS
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan 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-HTP / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsOikonomakos, N.G. / Heightman, T.D.
Citation
Journal: HELV.CHIM.ACTA / Year: 1998
Title: Cooperative interactions of the catalytic nucleophile and the catalytic acid in the inhibition of beta-glycosidases. Calculations and their validation by comparative kinetic and structural ...Title: Cooperative interactions of the catalytic nucleophile and the catalytic acid in the inhibition of beta-glycosidases. Calculations and their validation by comparative kinetic and structural studies of the inhibition of glycogen phosphorylase b.
Authors: Heightman, T.D. / Vasella, A. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Oikonomakos, N.G.
#1: Journal: Biochemistry / Year: 1996
Title: Ternary Complex Crystal Structures of Glycogen Phosphorylase with the Transition State Analogue Nojirimycin Tetrazole and Phosphate in the T and R States
Authors: Mitchell, E.P. / Withers, S.G. / Ermert, P. / Vasella, A.T. / Garman, E.F. / Oikonomakos, N.G. / Johnson, L.N.
#2: Journal: Glycogen Phosphorylase B: Description of the Protein Structure
Year: 1991
Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N.
History
DepositionOct 20, 1997-
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9305
Polymers97,2911
Non-polymers6394
Water9,008500
1
A: GLYCOGEN PHOSPHORYLASE
hetero molecules

A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,86110
Polymers194,5822
Non-polymers1,2798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8350 Å2
ΔGint-44 kcal/mol
Surface area56740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.720, 126.720, 115.590
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 /


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-HTP / 4,5,6-TRIHYDROXY-7-HYDROXYMETHYL-4,5,6,7-TETRAHYDRO-1H-[1,2,3]TRIAZOLO[1,5-A]PYRIDIN-8-YLIUM


Mass: 202.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12N3O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growMethod: soak native crystals / pH: 6.7
Details: NATIVE T-STATE GLYCOGEN PHOSPHORYLASE CRYSTALS WERE SOAKED WITH 10 MM BES, 0.1 MM EDTA AND 0.02% SODIUM AZIDE SOLUTION CONTAINING 5 MM TRIAZOLE AND 50 MM SODIUM DIHYDROGEN PHOSPHATE FOR 1 ...Details: NATIVE T-STATE GLYCOGEN PHOSPHORYLASE CRYSTALS WERE SOAKED WITH 10 MM BES, 0.1 MM EDTA AND 0.02% SODIUM AZIDE SOLUTION CONTAINING 5 MM TRIAZOLE AND 50 MM SODIUM DIHYDROGEN PHOSPHATE FOR 1 HOUR., pH 6.7, soak native crystals
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127-28 mg/mlGPb11
21 mMspermine11
33 mMdithiothreitol11
410 mMBES11
50.1 mMEDTA11
60.02 %sodium azide11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 37906 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.4
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.9 / % possible all: 76.1
Reflection shell
*PLUS
% possible obs: 76.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / Rfactor Rfree error: 0.0034 / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.276 -10 %
Rwork0.203 --
obs0.203 35849 84.9 %
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 39 500 7281
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_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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