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- PDB-7p7d: Rabbit muscle Glycogen Phosphorylase T state -

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Basic information

Entry
Database: PDB / ID: 7p7d
TitleRabbit muscle Glycogen Phosphorylase T state
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / Glycogen metabolism
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.
Similarity search - Domain/homology
Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsStravodimos, G.A. / Leonidas, D.D.
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
DepositionJul 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
SupersessionOct 13, 2021ID: 7O8E
Revision 1.1Oct 13, 2021Group: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_PDB_obs_spr / pdbx_database_proc
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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)97,83922
Polymers96,1981
Non-polymers1,64121
Water14,304794
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,67744
Polymers192,3962
Non-polymers3,28242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)126.279, 126.279, 115.361
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1026-

HOH

21A-1478-

HOH

31A-1533-

HOH

41A-1720-

HOH

51A-1778-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 96197.836 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 6.7 / Details: 10 mM BES buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2019
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→115.36 Å / Num. obs: 164062 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.032 / Rrim(I) all: 0.086 / Net I/σ(I): 13.6 / Num. measured all: 1196324
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.477.50.6625969579950.940.2590.711399.9
7.94-115.366.50.087760511710.990.0360.09525.399.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPB

1gpb


Resolution: 1.45→70.71 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.877 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 8292 5.1 %RANDOM
Rwork0.1301 ---
obs0.132 155665 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 102.29 Å2 / Biso mean: 26.003 Å2 / Biso min: 14.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2--1.63 Å2-0 Å2
3----3.25 Å2
Refinement stepCycle: final / Resolution: 1.45→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 84 794 7527
Biso mean--55.64 39.07 -
Num. residues----815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136913
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176655
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.6449337
X-RAY DIFFRACTIONr_angle_other_deg1.5151.57915221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53321.394416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.011151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1651563
X-RAY DIFFRACTIONr_chiral_restr0.0960.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021696
X-RAY DIFFRACTIONr_rigid_bond_restr2.764313567
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 599 -
Rwork0.228 11379 -
all-11978 -
obs--99.92 %

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