PDB-3e3l: The R-state Glycogen Phosphorylase

ID or keywords:

Entry

Database: PDB / ID: 3e3l

Title

The R-state Glycogen Phosphorylase

Components

Glycogen phosphorylase, muscle form

Keywords

TRANSFERASE /

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

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.59 Å

Authors

Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.

Citation

Journal: 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

Deposition	Aug 7, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 15, 2021	Group: 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 1.4	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3e3l.cif.gz	642.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3e3l.ent.gz	527.8 KB	Display	PDB format
PDBx/mmJSON format	3e3l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e3/3e3l ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e3l	HTTPS FTP

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Related structure data

Related structure data	3e3nC 3e3oC 7p7dC 9gpbS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3e3n-4 1gpa-3 1noi-2 1noi-1 1gpa-2 3e3o-2 3e3o-1 3e3n-1 1l5v-d 1fa9-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#24 - Dec 2001 Glycogen Phosphorylase similarity (7)

Deposited unit

A: Glycogen phosphorylase, muscle form

B: Glycogen phosphorylase, muscle form

C: Glycogen phosphorylase, muscle form

D: Glycogen phosphorylase, muscle form

hetero molecules

391 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycogen phosphorylase, muscle form

B: Glycogen phosphorylase, muscle form

hetero molecules

defined by author&software
196 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glycogen phosphorylase, muscle form

D: Glycogen phosphorylase, muscle form

hetero molecules

defined by author&software
196 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.895, 189.920, 88.160
Angle α, β, γ (deg.)	90.00, 109.27, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.93 %
Crystal grow	Temperature: 289 K / Method: small tubes / pH: 7.5 Details: 1.1-1.3 M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, SMALL TUBES, temperature 289K

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Data collection

Diffraction	Mean temperature: 293 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.97976 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2008
Radiation	Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97976 Å / Relative weight: 1
Reflection	Resolution: 2.59→30 Å / Num. all: 112937 / Num. obs: 107281 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / R_sym value: 0.064 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.89 / R_sym value: 0.358 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345		data collection
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: pdb entry 9gpb

9gpb

Resolution: 2.59→29.59 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.917 / SU B: 29.764 / SU ML: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.627 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26577	5654	5 %	RANDOM
R_work	0.20656	-	-	-
obs	0.20958	107281	99.29 %	-
all	-	107281	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 49.826 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.95 Å²	0 Å²	-0.36 Å²
2-	-	0 Å²	0 Å²
3-	-	-	1.71 Å²

Refine analyze

Luzzati coordinate error obs: 2.723 Å / Luzzati sigma a obs: 0.296 Å

Refinement step

Cycle: LAST / Resolution: 2.59→29.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26363	0	60	110	26533

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	26993
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.341	1.957	36528
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.261	5	3218
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.841	23.479	1374
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.501	15	4732
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.187	15	240
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	3939
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	20616
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	11998
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	17947
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	803
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.191	0.2	51
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.133	0.2	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.471	1.5	16490
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.851	2	25988
X-RAY DIFFRACTION	r_scbond_it	1.125	3	11866
X-RAY DIFFRACTION	r_scangle_it	1.889	4.5	10540
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.595→2.662 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.374	403	-
R_work	0.309	7636	-
obs	-	-	95.84 %

Refinement TLS params.

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

ID	L11 (°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)
1	3.6189	-2.1479	-2.6079	4.9023	2.3031	2.0366	-0.5252	0.0338	-0.4761	0.2496	0.2164	0.064	0.6039	0.2629	0.3088	0.0536	0.0776	-0.1939	-0.1416	-0.0514	0.4372	53.018	-24.4827	53.5074
2	2.955	0.0603	-0.5758	4.0634	3.5298	5.4012	0.1447	0.2016	-0.7235	-0.0586	-0.0293	-0.4352	-0.067	-0.0722	-0.1155	-0.0157	-0.0107	-0.0718	-0.0824	-0.0579	0.3915	50.8229	-12.5593	50.788
3	1.5719	0.9871	-0.9802	1.0895	-0.2715	2.1723	-0.0677	0.292	-0.5421	0.0937	0.0599	-0.3444	-0.1491	-0.1909	0.0079	-0.0534	0.0157	-0.0116	0.0245	-0.2071	0.3043	47.3237	-8.4567	37.4145
4	1.454	0.55	0.0007	0.9433	-0.7715	0.81	-0.1862	0.165	-0.4288	-0.0006	0.015	-0.2917	-0.0574	0.0772	0.1712	-0.0058	-0.0326	-0.0295	-0.0007	-0.1652	0.2665	61.3859	-0.3955	35.4507
5	6.296	2.0672	-0.4602	7.8684	1.2401	2.5724	0.455	-0.3708	0.0613	0.1064	-0.503	-0.4828	-0.4099	0.3736	0.048	0.0805	-0.0533	0.062	0.0062	-0.1308	0.0742	69.5073	11.4032	36.6834
6	2.291	0.9963	-0.5427	1.1534	-0.1793	2.8893	-0.2947	0.7377	-0.518	-0.1813	0.0129	-0.2884	-0.0225	-0.3245	0.2819	-0.1209	-0.0662	0.126	0.2586	-0.3985	0.2009	64.6644	-1.7633	13.5529
7	3.431	0.4531	-0.9406	1.6871	-0.0682	1.8571	-0.0833	0.2967	-0.5058	0.0844	0.2923	-0.1549	-0.0273	-0.0401	-0.209	-0.0422	-0.078	-0.0034	0.136	-0.1493	0.102	31.35	-7.3658	27.4561
8	2.1294	0.5826	0.4223	2.151	0.0044	1.2248	-0.1314	0.4486	0.1706	0.0598	0.2393	0.0757	-0.0418	-0.0526	-0.1079	-0.0231	-0.0493	0.0145	0.1753	0.0173	-0.0287	29.3889	12.2186	27.8775
9	2.1751	0.3102	0.1875	2.0483	-0.0573	0.4422	-0.2779	0.7999	0.0021	-0.2333	0.4088	0.0103	-0.0186	0.0038	-0.1309	-0.0338	-0.1721	-0.0019	0.3665	-0.0446	-0.1356	31.1118	7.6113	17.2073
10	9.9789	-5.4292	-2.1411	2.9705	1.2584	0.9848	-0.3198	-0.6554	-1.3945	0.4687	-0.0951	0.6645	0.1842	-0.0543	0.4148	0.0478	-0.0408	0.0125	-0.1056	0.0111	0.4816	50.4569	-19.3947	63.9531
11	1.2187	0.1473	0.1212	1.4848	1.0081	1.6733	0.1427	-0.0499	-0.556	0.0605	0.003	-0.0653	0.1557	0.0368	-0.1457	0.0443	-0.0046	-0.0747	-0.0618	0.0788	0.1842	67.1361	-9.882	65.1887
12	12.8723	2.1635	3.3938	0.3636	0.5704	0.8948	-0.1942	1.3922	-0.0568	-0.2568	0.183	0.1543	0.0199	0.392	0.0112	0.0973	0.0194	-0.0419	0.2292	-0.045	0.0626	82.6757	-0.8089	53.452
13	1.5722	0.4418	0.3558	3.6964	-1.4471	1.9528	0.0655	-0.003	-0.0572	0.0618	0.0244	0.4119	-0.2209	-0.1159	-0.0899	0.1077	-0.0045	0.0236	0.0556	0.047	0.0152	60.86	10.6849	62.5776
14	7.0852	-3.4597	6.3922	6.0378	-5.7935	15.7355	-0.0173	0.192	0.5029	-0.2791	-0.3998	0.0361	-0.3722	0.0129	0.4171	0.2285	-0.0582	0.1258	0.0305	-0.0033	-0.0332	68.5752	16.4729	47.8873
15	1.3429	0.2457	0.7142	1.8801	0.3882	2.9302	0.0032	-0.1157	0.0532	0.0454	0.0765	0.0793	-0.3181	0.0925	-0.0797	0.2003	0.0023	0.0675	0.0447	0.0377	-0.0339	68.2537	22.6153	74.4385
16	1.8433	-0.6535	0.2151	3.6546	0.2049	0.3567	0.1361	-0.2108	-0.4909	-0.1041	0.0459	-0.1223	0.0926	0.0906	-0.182	0.1488	-0.0452	-0.0169	0.0697	0.1099	0.0353	83.232	-4.7281	80.3406
17	1.8893	0.3217	-0.2577	1.7107	-0.8926	2.261	0.0396	-0.0138	-0.2403	0.1921	-0.1734	-0.4704	-0.3309	0.1816	0.1339	0.0791	-0.0241	-0.1322	-0.0598	0.0728	0.1126	102.0854	-1.8089	73.5097
18	2.2159	-1.5779	-1.1058	1.5011	-0.0349	2.3433	0.1565	-0.4247	-0.7634	0.2227	-0.1554	0.3331	0.4712	-0.5894	-0.0011	0.0935	-0.09	0.0282	0.1057	0.1645	0.0493	66.6502	-3.7806	84.4911
19	0.3119	0.3991	-1.1593	13.7472	16.3882	28.4365	-0.4797	0.8571	0.1459	-0.9786	0.645	-0.0402	-1.4764	1.8043	-0.1653	-0.1825	-0.0969	-0.0826	0.3318	0.2856	0.1853	103.6714	64.1198	18.195
20	1.8799	-0.618	-0.1427	1.9762	-0.0254	0.2673	-0.0399	0.2343	0.4149	0.1896	0.0314	0.0187	-0.1674	0.0009	0.0085	0.0707	-0.0877	-0.0402	0.0684	0.1183	0.0378	101.9105	54.218	34.2084
21	0.8581	-0.213	1.982	0.6499	-0.7424	4.683	0.1345	-0.2385	0.1861	0.4473	0.2133	0.2538	0.2827	-0.568	-0.3479	0.1429	-0.0802	0.0525	0.1026	0.0262	-0.0937	91.4896	45.4357	45.4968
22	1.4958	1.3702	0.4752	5.0797	0.2791	1.136	-0.0665	0.1465	0.067	-0.2054	-0.0001	0.3788	0.0899	-0.1422	0.0666	0.0863	-0.0369	0.0258	0.2249	0.0633	-0.0102	96.7065	32.1539	26.3364
23	4.4486	0.3939	-0.8335	2.5336	0.0348	2.0555	-0.0858	0.1343	-0.2027	0.0345	0.0176	0.1755	0.0792	-0.1867	0.0683	0.0991	-0.0341	-0.0097	0.1784	0.0232	0.0376	98.1002	29.5914	29.8912
24	0.6342	0.3002	-0.0605	2.3893	-0.2081	0.6684	-0.0431	-0.0438	-0.1858	0.2983	-0.0428	-0.3973	0.1753	0.2033	0.086	-0.013	0.0167	-0.0083	0.1534	0.0554	0.0264	113.4804	22.0816	38.5037
25	2.8944	0.5754	-1.2978	3.387	-0.2127	3.9131	0.1773	0.0035	0.5421	0.6205	-0.265	-0.033	-0.9186	0.1659	0.0877	0.3731	-0.2916	-0.2516	-0.0652	0.0962	0.0204	116.4346	61.238	55.2479
26	1.0632	0.2265	0.0712	1.2834	-0.5539	1.7112	0.1991	-0.193	-0.0521	0.7349	-0.2292	-0.1568	-0.1768	0.092	0.03	0.4289	-0.239	-0.1807	0.0058	0.0569	-0.0994	109.2923	41.5578	68.9956
27	1.4071	0.183	-0.2548	2.508	0.9372	2.6122	0.049	0.1782	0.1627	0.3024	-0.2143	-0.4756	-0.3321	0.3847	0.1653	0.0223	-0.1477	-0.134	0.1669	0.1745	0.1494	123.0672	48.7396	43.0614
28	2.4568	0.001	-0.3954	0.2268	-0.2012	1.1191	-0.2034	0.3538	0.8493	0.0862	0.1227	-0.0027	-0.1877	0.2251	0.0807	-0.0085	-0.102	-0.1037	0.038	0.2966	0.285	83.8203	62.4112	19.9108
29	1.8847	0.5709	0.0285	1.0959	-0.4023	1.1186	-0.1077	0.3506	0.3041	-0.0583	0.0895	0.108	0.0826	0.1404	0.0182	0.005	-0.0413	-0.0535	0.0232	0.2163	0.1739	73.554	51.0218	22.647
30	2.1388	0.9979	-2.7821	9.4532	-4.9773	5.1251	-0.2485	-0.0013	-0.1012	0.3094	-0.0582	-0.2666	0.3253	0.3681	0.3067	0.0981	0.0449	0.032	-0.0025	0.0575	0.0884	71.6223	37.0216	35.3195
31	1.2861	0.3185	-0.0086	0.8595	-0.1746	1.1339	-0.1028	0.1708	0.3616	0.0638	0.0047	0.2278	0.0282	-0.1339	0.0981	-0.0097	-0.0185	-0.0155	-0.0401	0.1569	0.3132	51.7351	53.4119	29.6383
32	2.5746	-0.2731	0.1704	3.6011	0.2208	2.2533	-0.3223	0.8956	0.0616	-0.101	0.3799	-0.0055	0.5239	-0.4498	-0.0576	-0.047	-0.3045	-0.0611	0.5805	0.2202	-0.1893	46.7904	31.4713	-2.1195

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 34
2	X-RAY DIFFRACTION	2	A	35 - 75
3	X-RAY DIFFRACTION	3	A	76 - 165
4	X-RAY DIFFRACTION	4	A	166 - 246
5	X-RAY DIFFRACTION	5	A	247 - 292
6	X-RAY DIFFRACTION	6	A	293 - 467
7	X-RAY DIFFRACTION	7	A	468 - 559
8	X-RAY DIFFRACTION	8	A	560 - 689
9	X-RAY DIFFRACTION	9	A	690 - 837
10	X-RAY DIFFRACTION	10	B	7 - 33
11	X-RAY DIFFRACTION	11	B	34 - 161
12	X-RAY DIFFRACTION	12	B	162 - 188
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18	X-RAY DIFFRACTION	18	B	810 - 839
19	X-RAY DIFFRACTION	19	C	9 - 28
20	X-RAY DIFFRACTION	20	C	29 - 163
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30	X-RAY DIFFRACTION	30	D	244 - 292
31	X-RAY DIFFRACTION	31	D	293 - 506
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