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- PDB-5mcb: Glycogen phosphorylase in complex with chlorogenic acid. -

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Basic information

Entry
Database: PDB / ID: 5mcb
TitleGlycogen phosphorylase in complex with chlorogenic acid.
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / alpha and beta protein
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
Chlorogenic acid / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLeonidas, D.D. / Stravodimos, G.A. / Kyriakis, E. / Chatzileontiadou, D.S.M. / Kantsadi, A.L.
CitationJournal: Curr Drug Discov Technol / Year: 2018
Title: Affinity Crystallography Reveals the Bioactive Compounds of Industrial Juicing Byproducts of Punica granatum for Glycogen Phosphorylase.
Authors: Stravodimos, G.A. / Kantsadi, A.L. / Apostolou, A. / Kyriakis, E. / Kafaski-Kanelli, V.N. / Solovou, T. / Gatzona, P. / Liggri, P.G.V. / Theofanous, S. / Gorgogietas, V.A. / Kissa, A. / ...Authors: Stravodimos, G.A. / Kantsadi, A.L. / Apostolou, A. / Kyriakis, E. / Kafaski-Kanelli, V.N. / Solovou, T. / Gatzona, P. / Liggri, P.G.V. / Theofanous, S. / Gorgogietas, V.A. / Kissa, A. / Psachoula, C. / Lemonakis, A. / Chatzileontiadou, D.S.M. / Psarra, A.G. / Skamnaki, V.T. / Haroutounian, S.A. / Leonidas, D.D.
History
DepositionNov 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)95,8823
Polymers95,2811
Non-polymers6012
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint0 kcal/mol
Surface area30840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.950, 128.950, 116.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1266-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form / / Myophosphorylase


Mass: 95280.914 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CGG / Chlorogenic acid / Chlorogenic acid


Mass: 354.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18O9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10mM BES Buffer

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 52193 / % possible obs: 100 % / Redundancy: 5.73 % / Rsym value: 0.101 / Net I/σ(I): 7.7
Reflection shellResolution: 1.95→1.98 Å / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTU

5jtu


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 6.786 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17744 2766 5 %RANDOM
Rwork0.13821 ---
obs0.14021 52193 76.32 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 35.949 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 40 267 6890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196772
X-RAY DIFFRACTIONr_bond_other_d0.0020.026467
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9589170
X-RAY DIFFRACTIONr_angle_other_deg0.978314807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0475806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79523.545347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.785151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5981559
X-RAY DIFFRACTIONr_chiral_restr0.090.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021651
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9391.9833234
X-RAY DIFFRACTIONr_mcbond_other2.8451.9813232
X-RAY DIFFRACTIONr_mcangle_it3.8332.9524036
X-RAY DIFFRACTIONr_mcangle_other3.8362.9534037
X-RAY DIFFRACTIONr_scbond_it5.0812.6243538
X-RAY DIFFRACTIONr_scbond_other5.0812.6243539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5553.7065135
X-RAY DIFFRACTIONr_long_range_B_refined9.16924.5857632
X-RAY DIFFRACTIONr_long_range_B_other9.16824.5857633
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 194 -
Rwork0.243 4083 -
obs--81.92 %
Refinement TLS params.Method: refined / Origin x: 28.357 Å / Origin y: 21.364 Å / Origin z: 31.726 Å
111213212223313233
T0.0503 Å2-0.0386 Å20.0027 Å2-0.0745 Å2-0.0217 Å2--0.014 Å2
L0.6384 °20.0332 °20.0417 °2-0.5433 °2-0.1749 °2--0.9779 °2
S-0.0361 Å °0.0233 Å °0.0532 Å °-0.0088 Å °0.0101 Å °0.0183 Å °0.0622 Å °-0.1005 Å °0.026 Å °

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