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- PDB-3g2n: Crystal structure of N-acylglucosylamine with glycogen phosphorylase -

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Basic information

Entry
Database: PDB / ID: 3g2n
TitleCrystal structure of N-acylglucosylamine with glycogen phosphorylase
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / Glycogen phosphorylase / amide-1 / 2 / 3-triazole bioisosterism / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / 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
N-(phenylcarbonyl)-beta-D-glucopyranosylamine / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChrysina, E.D. / Bokor, E. / Alexacou, K.-M. / Charavgi, M.-D. / Oikonomakos, G.N. / Zographos, S.E. / Leonidas, D.D. / Oikonomakos, N.G. / Somsak, L.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Glucose analogue inhibitors of glycogen phosphorylase: from crystallographic analysis to drug prediction using GRID force-field and GOLPE variable selection.
Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Cruciani, G. / Son, J.C. / Bichard, C.J. / Fleet, G.W. / Oikonomakos, N.G. / Kontou, M. / Zographos, S.E.
History
DepositionJan 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 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
Revision 1.4Nov 22, 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:
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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8032
Polymers97,5191
Non-polymers2831
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6054
Polymers195,0392
Non-polymers5672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5040 Å2
ΔGint-26.4 kcal/mol
Surface area56780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.639, 128.639, 116.353
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-OAK / N-(phenylcarbonyl)-beta-D-glucopyranosylamine / N-(phenylcarbonyl)-beta-D-glucosylamine / N-(phenylcarbonyl)-D-glucosylamine / N-(phenylcarbonyl)-glucosylamine


Type: D-saccharide / Mass: 283.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 292 K / Method: small tubes / pH: 6.8 / Details: pH 6.8, SMALL TUBES, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 56904 / % possible obs: 99 % / Redundancy: 5.6 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2851 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PRJ

2prj


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.484 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22734 2886 5.1 %RANDOM
Rwork0.19706 ---
obs0.19857 53971 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.689 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6653 0 20 228 6901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226824
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.9569236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.255813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5823.543350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.779151186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8361559
X-RAY DIFFRACTIONr_chiral_restr0.0760.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025234
X-RAY DIFFRACTIONr_nbd_refined0.1830.22914
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2324
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.22
X-RAY DIFFRACTIONr_mcbond_it0.6171.54193
X-RAY DIFFRACTIONr_mcangle_it1.07726556
X-RAY DIFFRACTIONr_scbond_it1.31433007
X-RAY DIFFRACTIONr_scangle_it2.1784.52680
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 216 -
Rwork0.243 3963 -
obs--99.98 %

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