[English] 日本語
Yorodumi
- PDB-3e3l: The R-state Glycogen Phosphorylase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e3l
TitleThe R-state Glycogen Phosphorylase
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 / : / : / 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
Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.59 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 1.0Feb 10, 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: 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 1.4Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)391,23016
Polymers390,0774
Non-polymers1,15312
Water1,982110
1
A: Glycogen phosphorylase, muscle form
B: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6158
Polymers195,0392
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-108 kcal/mol
Surface area61690 Å2
MethodPISA
2
C: Glycogen phosphorylase, muscle form
D: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6158
Polymers195,0392
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-94 kcal/mol
Surface area61330 Å2
MethodPISA
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 number4
Space group name H-MP1211

-
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: muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 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

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.97976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2008
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 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 % / Rsym value: 0.064 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.89 / Rsym value: 0.358 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 9gpb
Resolution: 2.59→29.59 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.26577 5654 5 %RANDOM
Rwork0.20656 ---
obs0.20958 107281 99.29 %-
all-107281 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.826 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å2-0.36 Å2
2--0 Å20 Å2
3---1.71 Å2
Refine analyzeLuzzati coordinate error obs: 2.723 Å / Luzzati sigma a obs: 0.296 Å
Refinement stepCycle: LAST / Resolution: 2.59→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26363 0 60 110 26533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02226993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.95736528
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26153218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84123.4791374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.501154732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.18715240
X-RAY DIFFRACTIONr_chiral_restr0.0960.23939
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220616
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.211998
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.217947
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2803
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4711.516490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.851225988
X-RAY DIFFRACTIONr_scbond_it1.125311866
X-RAY DIFFRACTIONr_scangle_it1.8894.510540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.595→2.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 403 -
Rwork0.309 7636 -
obs--95.84 %
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)
13.6189-2.1479-2.60794.90232.30312.0366-0.52520.0338-0.47610.24960.21640.0640.60390.26290.30880.05360.0776-0.1939-0.1416-0.05140.437253.018-24.482753.5074
22.9550.0603-0.57584.06343.52985.40120.14470.2016-0.7235-0.0586-0.0293-0.4352-0.067-0.0722-0.1155-0.0157-0.0107-0.0718-0.0824-0.05790.391550.8229-12.559350.788
31.57190.9871-0.98021.0895-0.27152.1723-0.06770.292-0.54210.09370.0599-0.3444-0.1491-0.19090.0079-0.05340.0157-0.01160.0245-0.20710.304347.3237-8.456737.4145
41.4540.550.00070.9433-0.77150.81-0.18620.165-0.4288-0.00060.015-0.2917-0.05740.07720.1712-0.0058-0.0326-0.0295-0.0007-0.16520.266561.3859-0.395535.4507
56.2962.0672-0.46027.86841.24012.57240.455-0.37080.06130.1064-0.503-0.4828-0.40990.37360.0480.0805-0.05330.0620.0062-0.13080.074269.507311.403236.6834
62.2910.9963-0.54271.1534-0.17932.8893-0.29470.7377-0.518-0.18130.0129-0.2884-0.0225-0.32450.2819-0.1209-0.06620.1260.2586-0.39850.200964.6644-1.763313.5529
73.4310.4531-0.94061.6871-0.06821.8571-0.08330.2967-0.50580.08440.2923-0.1549-0.0273-0.0401-0.209-0.0422-0.078-0.00340.136-0.14930.10231.35-7.365827.4561
82.12940.58260.42232.1510.00441.2248-0.13140.44860.17060.05980.23930.0757-0.0418-0.0526-0.1079-0.0231-0.04930.01450.17530.0173-0.028729.388912.218627.8775
92.17510.31020.18752.0483-0.05730.4422-0.27790.79990.0021-0.23330.40880.0103-0.01860.0038-0.1309-0.0338-0.1721-0.00190.3665-0.0446-0.135631.11187.611317.2073
109.9789-5.4292-2.14112.97051.25840.9848-0.3198-0.6554-1.39450.4687-0.09510.66450.1842-0.05430.41480.0478-0.04080.0125-0.10560.01110.481650.4569-19.394763.9531
111.21870.14730.12121.48481.00811.67330.1427-0.0499-0.5560.06050.003-0.06530.15570.0368-0.14570.0443-0.0046-0.0747-0.06180.07880.184267.1361-9.88265.1887
1212.87232.16353.39380.36360.57040.8948-0.19421.3922-0.0568-0.25680.1830.15430.01990.3920.01120.09730.0194-0.04190.2292-0.0450.062682.6757-0.808953.452
131.57220.44180.35583.6964-1.44711.95280.0655-0.003-0.05720.06180.02440.4119-0.2209-0.1159-0.08990.1077-0.00450.02360.05560.0470.015260.8610.684962.5776
147.0852-3.45976.39226.0378-5.793515.7355-0.01730.1920.5029-0.2791-0.39980.0361-0.37220.01290.41710.2285-0.05820.12580.0305-0.0033-0.033268.575216.472947.8873
151.34290.24570.71421.88010.38822.93020.0032-0.11570.05320.04540.07650.0793-0.31810.0925-0.07970.20030.00230.06750.04470.0377-0.033968.253722.615374.4385
161.8433-0.65350.21513.65460.20490.35670.1361-0.2108-0.4909-0.10410.0459-0.12230.09260.0906-0.1820.1488-0.0452-0.01690.06970.10990.035383.232-4.728180.3406
171.88930.3217-0.25771.7107-0.89262.2610.0396-0.0138-0.24030.1921-0.1734-0.4704-0.33090.18160.13390.0791-0.0241-0.1322-0.05980.07280.1126102.0854-1.808973.5097
182.2159-1.5779-1.10581.5011-0.03492.34330.1565-0.4247-0.76340.2227-0.15540.33310.4712-0.5894-0.00110.0935-0.090.02820.10570.16450.049366.6502-3.780684.4911
190.31190.3991-1.159313.747216.388228.4365-0.47970.85710.1459-0.97860.645-0.0402-1.47641.8043-0.1653-0.1825-0.0969-0.08260.33180.28560.1853103.671464.119818.195
201.8799-0.618-0.14271.9762-0.02540.2673-0.03990.23430.41490.18960.03140.0187-0.16740.00090.00850.0707-0.0877-0.04020.06840.11830.0378101.910554.21834.2084
210.8581-0.2131.9820.6499-0.74244.6830.1345-0.23850.18610.44730.21330.25380.2827-0.568-0.34790.1429-0.08020.05250.10260.0262-0.093791.489645.435745.4968
221.49581.37020.47525.07970.27911.136-0.06650.14650.067-0.2054-0.00010.37880.0899-0.14220.06660.0863-0.03690.02580.22490.0633-0.010296.706532.153926.3364
234.44860.3939-0.83352.53360.03482.0555-0.08580.1343-0.20270.03450.01760.17550.0792-0.18670.06830.0991-0.0341-0.00970.17840.02320.037698.100229.591429.8912
240.63420.3002-0.06052.3893-0.20810.6684-0.0431-0.0438-0.18580.2983-0.0428-0.39730.17530.20330.086-0.0130.0167-0.00830.15340.05540.0264113.480422.081638.5037
252.89440.5754-1.29783.387-0.21273.91310.17730.00350.54210.6205-0.265-0.033-0.91860.16590.08770.3731-0.2916-0.2516-0.06520.09620.0204116.434661.23855.2479
261.06320.22650.07121.2834-0.55391.71120.1991-0.193-0.05210.7349-0.2292-0.1568-0.17680.0920.030.4289-0.239-0.18070.00580.0569-0.0994109.292341.557868.9956
271.40710.183-0.25482.5080.93722.61220.0490.17820.16270.3024-0.2143-0.4756-0.33210.38470.16530.0223-0.1477-0.1340.16690.17450.1494123.067248.739643.0614
282.45680.001-0.39540.2268-0.20121.1191-0.20340.35380.84930.08620.1227-0.0027-0.18770.22510.0807-0.0085-0.102-0.10370.0380.29660.28583.820362.411219.9108
291.88470.57090.02851.0959-0.40231.1186-0.10770.35060.3041-0.05830.08950.1080.08260.14040.01820.005-0.0413-0.05350.02320.21630.173973.55451.021822.647
302.13880.9979-2.78219.4532-4.97735.1251-0.2485-0.0013-0.10120.3094-0.0582-0.26660.32530.36810.30670.09810.04490.032-0.00250.05750.088471.622337.021635.3195
311.28610.3185-0.00860.8595-0.17461.1339-0.10280.17080.36160.06380.00470.22780.0282-0.13390.0981-0.0097-0.0185-0.0155-0.04010.15690.313251.735153.411929.6383
322.5746-0.27310.17043.60110.22082.2533-0.32230.89560.0616-0.1010.3799-0.00550.5239-0.4498-0.0576-0.047-0.3045-0.06110.58050.2202-0.189346.790431.4713-2.1195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 34
2X-RAY DIFFRACTION2A35 - 75
3X-RAY DIFFRACTION3A76 - 165
4X-RAY DIFFRACTION4A166 - 246
5X-RAY DIFFRACTION5A247 - 292
6X-RAY DIFFRACTION6A293 - 467
7X-RAY DIFFRACTION7A468 - 559
8X-RAY DIFFRACTION8A560 - 689
9X-RAY DIFFRACTION9A690 - 837
10X-RAY DIFFRACTION10B7 - 33
11X-RAY DIFFRACTION11B34 - 161
12X-RAY DIFFRACTION12B162 - 188
13X-RAY DIFFRACTION13B189 - 249
14X-RAY DIFFRACTION14B250 - 281
15X-RAY DIFFRACTION15B288 - 436
16X-RAY DIFFRACTION16B437 - 560
17X-RAY DIFFRACTION17B561 - 809
18X-RAY DIFFRACTION18B810 - 839
19X-RAY DIFFRACTION19C9 - 28
20X-RAY DIFFRACTION20C29 - 163
21X-RAY DIFFRACTION21C164 - 194
22X-RAY DIFFRACTION22C195 - 253
23X-RAY DIFFRACTION23C254 - 338
24X-RAY DIFFRACTION24C339 - 499
25X-RAY DIFFRACTION25C500 - 560
26X-RAY DIFFRACTION26C561 - 739
27X-RAY DIFFRACTION27C795 - 837
28X-RAY DIFFRACTION28D8 - 102
29X-RAY DIFFRACTION29D103 - 243
30X-RAY DIFFRACTION30D244 - 292
31X-RAY DIFFRACTION31D293 - 506
32X-RAY DIFFRACTION32D703 - 771

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more