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- PDB-3e3n: The Glycogen phosphorylase b R state- AMP complex -

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Basic information

Entry
Database: PDB / ID: 3e3n
TitleThe Glycogen phosphorylase b R state- AMP complex
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / GLYCOGENOLYSIS / INHIBITION / TYPE 2 DIABETES / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate
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
ADENOSINE MONOPHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLeonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Glycogen phosphorylase revisited: extending the resolution of the R- and T-state structures of the free enzyme and in complex with allosteric activators.
Authors: Leonidas, D.D. / Zographos, S.E. / Tsitsanou, K.E. / Skamnaki, V.T. / Stravodimos, G. / Kyriakis, E.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 21, 2012Group: Atomic model
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 15, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
B: Glycogen phosphorylase, muscle form
C: Glycogen phosphorylase, muscle form
D: Glycogen phosphorylase, muscle form
E: Glycogen phosphorylase, muscle form
F: Glycogen phosphorylase, muscle form
G: Glycogen phosphorylase, muscle form
H: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)784,46932
Polymers780,1558
Non-polymers4,31524
Water6,305350
1
A: Glycogen phosphorylase, muscle form
B: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1178
Polymers195,0392
Non-polymers1,0796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-79 kcal/mol
Surface area60010 Å2
MethodPISA
2
C: Glycogen phosphorylase, muscle form
D: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1178
Polymers195,0392
Non-polymers1,0796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-82 kcal/mol
Surface area59570 Å2
MethodPISA
3
E: Glycogen phosphorylase, muscle form
F: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1178
Polymers195,0392
Non-polymers1,0796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-83 kcal/mol
Surface area59880 Å2
MethodPISA
4
G: Glycogen phosphorylase, muscle form
H: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1178
Polymers195,0392
Non-polymers1,0796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-83 kcal/mol
Surface area60070 Å2
MethodPISA
5
A: Glycogen phosphorylase, muscle form
B: Glycogen phosphorylase, muscle form
C: Glycogen phosphorylase, muscle form
D: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,23516
Polymers390,0774
Non-polymers2,15712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20190 Å2
ΔGint-179 kcal/mol
Surface area115350 Å2
MethodPISA
6
E: Glycogen phosphorylase, muscle form
F: Glycogen phosphorylase, muscle form
G: Glycogen phosphorylase, muscle form
H: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,23516
Polymers390,0774
Non-polymers2,15712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20490 Å2
ΔGint-182 kcal/mol
Surface area115460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.019, 188.079, 175.913
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 97519.320 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 7.5
Details: 1.2-1.4 M ammonium sulphate, pH 7.5, MICRODIALYSIS, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2002
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.7→29.85 Å / Num. all: 189203 / Num. obs: 189160 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.09 / Net I/σ(I): 6.2
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.67 / Rsym value: 0.521 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1abb

1abb


Resolution: 2.7→29.79 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 30.428 / SU ML: 0.29 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25609 9450 5 %RANDOM
Rwork0.19193 ---
obs0.19517 179705 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.03 Å2
2---0.11 Å20 Å2
3---0 Å2
Refine analyzeLuzzati sigma a obs: 0.292 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52898 0 264 350 53512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02254340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.96173562
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91556464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47623.4042750
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.633159516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.45915492
X-RAY DIFFRACTIONr_chiral_restr0.0960.27928
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0241486
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.224018
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.236356
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.21657
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5181.533104
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.873252182
X-RAY DIFFRACTIONr_scbond_it1.045324030
X-RAY DIFFRACTIONr_scangle_it1.7634.521380
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 664 -
Rwork0.289 12819 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.23-0.11160.19060.7832-0.21880.7611-0.03080.09040.1211-0.06960.046-0.02510.00450.0466-0.01520.0593-0.04260.01650.0554-0.0280.0534-27.439-23.606269.3126
21.24710.23840.33111.3189-0.01210.83510.07490.0277-0.05520.1184-0.0755-0.1637-0.0010.08820.00060.0906-0.04540.01410.12990.04310.01066.5994-21.1782113.1372
30.73470.32830.10751.37280.18091.08760.1073-0.114-0.01480.3136-0.1443-0.0637-0.0060.0850.0370.0616-0.0806-0.00260.24290.03740.085234.213917.566987.697
40.76720.12740.03740.8258-0.0681.6518-0.02670.0623-0.0029-0.1050.0255-0.0030.2117-0.02640.00130.0979-0.00210.0187-0.00310.04430.0852-10.982126.407255.4493
50.6250.27880.07461.26930.17231.14430.0617-0.0614-0.04310.2784-0.0442-0.15910.02270.0892-0.01750.0324-0.0196-0.03210.1830.01560.13235.584617.8065171.5055
60.78280.1626-0.04350.9477-0.19641.4852-0.02410.1522-0.0252-0.15380.05760.0240.2599-0.0667-0.03350.131-0.0120.00990.06890.05350.1139-39.61627.4486139.6354
71.37290.12070.04170.7766-0.11270.6334-0.08520.17960.1435-0.07370.0942-0.0128-0.03620.0139-0.0090.0567-0.05380.02650.0602-0.03860.0316-56.0205-22.6531151.6738
81.21310.18260.20351.5049-0.05890.6260.040.0312-0.14170.1207-0.0405-0.3385-0.02820.06420.00050.0533-0.0247-0.02730.03010.03440.0677-22.0173-21.4676195.7991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 837
2X-RAY DIFFRACTION2B7 - 837
3X-RAY DIFFRACTION3C9 - 837
4X-RAY DIFFRACTION4D7 - 838
5X-RAY DIFFRACTION5E8 - 837
6X-RAY DIFFRACTION6F8 - 837
7X-RAY DIFFRACTION7G7 - 837
8X-RAY DIFFRACTION8H6 - 836

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