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- PDB-3e3o: Glycogen phosphorylase R state-IMP complex -

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Basic information

Entry
Database: PDB / ID: 3e3o
TitleGlycogen phosphorylase R state-IMP 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
INOSINIC ACID / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 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 / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 15, 2021Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,23916
Polymers390,0774
Non-polymers2,16112
Water2,090116
1
A: Glycogen phosphorylase, muscle form
B: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1198
Polymers195,0392
Non-polymers1,0816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-81 kcal/mol
Surface area60850 Å2
MethodPISA
2
C: Glycogen phosphorylase, muscle form
D: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1198
Polymers195,0392
Non-polymers1,0816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-81 kcal/mol
Surface area60420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.680, 188.448, 87.853
Angle α, β, γ (deg.)90.00, 109.10, 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.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 48.32 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 7.5
Details: 1.1-1.3M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, MICRODIALYSIS, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8063 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2006
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8063 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. all: 111241 / Num. obs: 105631 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 65.109 Å2 / Rsym value: 0.061 / Net I/σ(I): 7.07
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.62 / Num. unique all: 5388 / Rsym value: 0.441 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2abb
Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 31.917 / SU ML: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26703 5573 5 %RANDOM
Rwork0.20073 ---
obs0.20405 105631 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.071 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å2-0.37 Å2
2--0.15 Å20 Å2
3---1.8 Å2
Refine analyzeLuzzati sigma a obs: 0.312 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26382 0 132 116 26630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02227096
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9636680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27953220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78123.4641374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.193154739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.98715241
X-RAY DIFFRACTIONr_chiral_restr0.0980.23958
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220669
X-RAY DIFFRACTIONr_nbd_refined0.2170.212352
X-RAY DIFFRACTIONr_nbtor_refined0.310.218056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2868
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.25
X-RAY DIFFRACTIONr_mcbond_it0.4621.516482
X-RAY DIFFRACTIONr_mcangle_it0.827226009
X-RAY DIFFRACTIONr_scbond_it1.089312003
X-RAY DIFFRACTIONr_scangle_it1.8114.510671
LS refinement shellResolution: 2.597→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 414 -
Rwork0.27 7369 -
obs--94.5 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.90070.7011-2.10910.5458-1.64184.93890.12750.5962-0.3502-0.4008-0.2017-0.36260.581-0.41360.07420.15330.0822-0.1191-0.1223-0.34530.972956.6782-28.310350.75
21.7050.3248-0.48041.97332.17244.74-0.00880.0885-0.69090.0899-0.0124-0.16250.08220.12430.02120.07890.0084-0.03880.0455-0.10480.435750.325-13.484451.5494
31.44880.7836-0.61620.8504-0.26471.913-0.07440.2713-0.42260.05430.0221-0.1088-0.0667-0.21640.05230.10360.00370.00360.1503-0.20370.336846.7341-8.808137.3986
44.2128-3.78033.14384.0972-3.45962.9245-0.4265-0.12860.43690.50450.0948-0.6013-0.2985-0.12590.33170.1881-0.0109-0.09630.1681-0.12690.221148.05711.761840.8085
53.2261-0.54151.2655-0.45671.3945-0.0960.1811-0.4949-0.0885-0.1154-0.2270.01460.18870.21140.15710.01160.00220.1242-0.16710.289866.8811-5.183733.0949
66.75912.5105-1.0727.7741.87553.49790.4015-0.15870.10650.4405-0.2246-0.3645-0.45830.4182-0.17690.2321-0.0258-0.02630.096-0.08640.077269.338511.21435.8738
73.1251.1251-1.28241.342-0.74291.7192-0.24270.4164-0.9448-0.0889-0.0914-0.23530.15880.00710.33410.0945-0.03620.08160.2268-0.30210.357968.2561-8.961922.0731
81.61930.7303-0.11921.24990.24313.1424-0.17291.0277-0.2466-0.18080.0184-0.02-0.3146-0.19230.15450.0421-0.02510.04650.5271-0.31560.094665.2192.11468.9271
94.07751.015-2.63170.9531-0.94632.9214-0.23581.2319-0.44-0.3070.2632-0.0828-0.0166-0.3916-0.02750.0154-0.13360.02480.5561-0.3840.085145.8677-4.971613.4151
104.20980.48-0.56245.64381.6723.15460.05950.0302-0.43520.39310.11150.15850.0466-0.1731-0.1710.0742-0.05570.00550.2124-0.05480.164823.7751-7.401833.2811
112.31540.3650.50761.709-0.00291.1391-0.09880.37790.2320.04090.15150.0797-0.0645-0.0078-0.05280.0726-0.03310.00160.2588-0.04190.114829.439612.221827.5764
122.12540.23110.27721.43570.27810.6204-0.22770.8335-0.0403-0.19150.26480.1669-0.0774-0.0091-0.03710.0428-0.1436-0.01550.4675-0.10220.016631.00537.593817.1774
136.7782-3.4549-2.2285.82462.16760.9945-0.0782-0.6235-1.50560.5502-0.2420.37340.1207-0.22040.32020.0879-0.0967-0.02860.08140.06820.427450.6274-19.000163.6907
142.7232-0.00010.53112.11780.97882.5110.10280.1032-0.7046-0.0026-0.0652-0.10390.00410.2228-0.03760.1582-0.0244-0.03370.0107-0.06940.432163.8773-16.41954.8411
151.58470.28890.09161.87831.02581.49520.1279-0.1101-0.56110.03080.0168-0.27470.19770.1139-0.14470.1540.004-0.04510.05910.06150.207268.5227-7.175368.8455
1638.39284.47724.77270.52210.55660.5933-0.34151.10270.3617-0.3850.05970.04970.32680.29760.28180.16620.0465-0.00050.28750.02220.106385.08830.350253.2358
171.82420.40520.37972.863-0.66521.36370.01360.0461-0.06370.09810.06510.3488-0.1981-0.0588-0.07870.2316-0.01730.03810.15820.01370.089961.46499.417462.4305
182.8559-3.47991.39959.0025-4.591110.99970.19980.68480.4294-0.8472-0.5123-0.2804-0.19690.11850.31260.3543-0.1040.11440.17330.0235-0.002367.61916.354147.9021
191.63960.21130.51982.00730.15872.9133-0.0121-0.17670.09390.06950.07590.104-0.23620.061-0.06370.2584-0.00660.050.1658-0.00430.059866.653820.77173.4404
201.57130.37660.55692.16120.99511.20060.0004-0.31470.01660.0640.0654-0.2437-0.18840.1181-0.06590.2199-0.04730.06180.2446-0.00690.052979.596715.839381.8711
215.5593-0.8509-2.52144.7502-0.41775.18570.0481-0.2297-1.1356-0.20160.1523-0.30680.4399-0.0851-0.20030.099-0.068-0.1418-0.08110.13430.42187.1421-20.181977.8606
222.65840.68790.30581.1637-0.94232.56940.02510.0631-0.5410.016-0.1055-0.4364-0.10750.04960.08040.11290.0144-0.03840.04080.0060.264899.4562-4.958769.349
232.12980.5839-0.72832.3003-1.01822.00030.0745-0.2218-0.10420.3528-0.2818-0.6499-0.76150.35750.20730.2287-0.0862-0.26880.0470.12910.2165106.9976.631474.5089
242.7314-0.8173-0.41870.8228-0.1711.40320.0786-0.5559-0.53980.3222-0.0438-0.25890.13360.0676-0.03480.2229-0.0445-0.12650.10870.15320.267486.9648-7.204984.0467
250.9774-2.2286-4.74111.727314.763725.3489-0.57040.83690.7085-0.50280.25770.0343-0.92391.26260.3126-0.0478-0.1876-0.09720.46690.33960.3527103.392963.447618.223
261.5396-0.61770.21352.29750.01740.1709-0.01330.16860.47240.23770.05460.0804-0.17520.0858-0.04140.1447-0.08020.01840.12760.07940.1733101.565853.675234.0425
272.4109-1.08815.12530.4911-2.313110.89570.1605-0.32630.34250.5249-0.02310.2254-0.1636-1.158-0.13750.2527-0.05680.12740.306500.101790.215244.294950.076
281.54940.99990.29163.7783-0.35150.6678-0.03560.16170.1138-0.297-0.03580.1380.05360.00750.07140.1529-0.03430.03890.2880.05030.06697.880333.66126.5555
2919.94378.63774.87919.83873.03685.75680.04090.89760.39690.032-0.31391.23030.3953-0.36460.2730.0792-0.01630.11260.3042-0.02680.111681.619728.857933.1727
302.16440.10210.23792.86380.10551.141-0.0660.1032-0.07530.00270.0917-0.20630.14780.1115-0.02570.1163-0.0050.00780.2584-0.03040.0938107.620622.634230.3917
311.6142-0.4135-0.26644.10290.44021.0049-0.00150.0034-0.22770.43220.0239-0.52160.17480.2807-0.02240.14230.0039-0.0930.26830.03610.0982117.88324.656943.3806
322.0748-0.2874-1.24643.44221.19513.87780.07090.02360.73330.486-0.12950.0739-0.78120.18410.05860.3673-0.2785-0.12290.0041-0.00040.1486116.196460.975754.6754
332.17460.4417-0.05981.3703-0.48742.33530.2946-0.26870.10510.6809-0.2672-0.0118-0.32390.0992-0.02740.4333-0.2231-0.07740.0947-0.03230.0152107.693445.45565.0469
341.78422.7409-1.84244.5877-1.98243.80970.285-0.1833-0.02521.0033-0.291-0.75970.08160.47480.0060.4848-0.285-0.45030.20080.1141-0.0163117.06732.375373.3835
353.34470.6853-0.27793.4725-1.32771.33130.5598-0.7742-0.10790.8644-0.43-0.1534-0.08360.1352-0.12980.6066-0.3082-0.18560.1783-0.0399-0.1635107.706438.890574.1449
362.4340.9965-0.65152.86611.93622.82550.27820.02180.35320.2321-0.0992-0.5258-0.26030.3598-0.1790.1532-0.1212-0.0770.25110.04650.2313122.663648.082741.9754
373.7312-2.1503-3.04612.71288.062929.485-0.23370.28330.9779-0.1181-0.05010.267-1.1649-1.23750.28380.142-0.2244-0.0686-0.19920.2660.748190.067272.367922.7203
382.8260.0531-0.45190.07970.27871.1203-0.14030.40660.7569-0.02570.10570.0978-0.09760.170.03460.0991-0.0708-0.0240.10770.32850.414981.774959.28118.8691
391.15220.50610.14230.63490.47631.215-0.0020.5830.2895-0.11470.05470.11670.16740.235-0.05280.1031-0.0387-0.02460.23310.27020.280775.557348.965913.5883
402.70091.223-0.95512.1813-2.06093.62040.1441-0.12110.54880.32790.04440.1153-0.26550.0671-0.18850.1751-0.0037-0.00030.00520.0960.376869.85452.242635.4928
413.0099-1.2795-2.36227.4859-2.52543.6926-0.2667-0.0474-0.15210.1714-0.1493-0.110.59110.42320.41590.22590.01960.10180.04590.08990.215470.794736.820135.1228
421.67190.26140.60162.1903-0.62580.8791-0.03150.00410.6880.2795-0.00170.0243-0.1031-0.03360.03320.1134-0.00590.032-0.00280.11810.48657.823257.508337.2223
431.7590.1971-0.13140.8974-0.41281.4369-0.02380.30010.4788-0.00910.00240.1730.1046-0.22570.02150.083-0.0351-0.0060.07470.17840.422247.745150.640225.233
442.4524-0.1362-0.34773.50261.79672.125-0.44990.52490.2388-0.44150.37740.1476-0.10790.5590.07250.1506-0.0380.07050.45950.51820.230767.708957.8072-7.2134
452.4972-0.09820.41513.5216-0.06313.32030.04091.07160.0743-0.5719-0.0107-0.18540.3726-0.0038-0.03020.1646-0.0780.02330.57440.2145-0.132760.518734.2637-5.9525
460.11280.34620.17892.3983-1.05062.201-0.19071.11361.1647-0.15440.1379-0.10130.2208-0.15330.05280.0333-0.05690.01460.49110.4880.266658.103849.52232.06
471.2869-0.41620.19793.7735-1.19491.8586-0.00381.19830.1808-0.39920.26160.35760.3992-0.5134-0.2578-0.0257-0.2197-0.14040.73660.2636-0.04644.105135.31-3.9931
481.90970.41470.2221.25880.38961.6543-0.00960.95580.563-0.23790.0574-0.03610.1439-0.1524-0.0478-0.0017-0.038-0.04540.48530.45780.179655.013848.90231.0131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 257 - 25
2X-RAY DIFFRACTION2AA26 - 7626 - 76
3X-RAY DIFFRACTION3AA77 - 16177 - 161
4X-RAY DIFFRACTION4AA162 - 187162 - 187
5X-RAY DIFFRACTION5AA188 - 246188 - 246
6X-RAY DIFFRACTION6AA247 - 294247 - 294
7X-RAY DIFFRACTION7AA295 - 360295 - 360
8X-RAY DIFFRACTION8AA361 - 452361 - 452
9X-RAY DIFFRACTION9AA453 - 497453 - 497
10X-RAY DIFFRACTION10AA498 - 560498 - 560
11X-RAY DIFFRACTION11AA561 - 691561 - 691
12X-RAY DIFFRACTION12AA692 - 837692 - 837
13X-RAY DIFFRACTION13BB7 - 337 - 33
14X-RAY DIFFRACTION14BB34 - 6734 - 67
15X-RAY DIFFRACTION15BB68 - 16168 - 161
16X-RAY DIFFRACTION16BB162 - 184162 - 184
17X-RAY DIFFRACTION17BB185 - 246185 - 246
18X-RAY DIFFRACTION18BB247 - 281247 - 281
19X-RAY DIFFRACTION19BB287 - 418287 - 418
20X-RAY DIFFRACTION20BB419 - 498419 - 498
21X-RAY DIFFRACTION21BB499 - 559499 - 559
22X-RAY DIFFRACTION22BB560 - 694560 - 694
23X-RAY DIFFRACTION23BB695 - 773695 - 773
24X-RAY DIFFRACTION24BB774 - 837774 - 837
25X-RAY DIFFRACTION25CC9 - 289 - 28
26X-RAY DIFFRACTION26CC29 - 16329 - 163
27X-RAY DIFFRACTION27CC164 - 188164 - 188
28X-RAY DIFFRACTION28CC189 - 248189 - 248
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