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- PDB-6eqj: Crystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant... -

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Basic information

Entry
Database: PDB / ID: 6eqj
TitleCrystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant, apo form
ComponentsGlycogenin-1
KeywordsHYDROLASE / glycogenin-1
Function / homology
Function and homology information


Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora ...Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis / lysosomal lumen / manganese ion binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / protein homodimerization activity / extracellular region / membrane / cytoplasm / cytosol
Similarity search - Function
Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 Å
AuthorsBailey, H.J. / Kopec, J. / Bilyard, M.K. / Bezerra, G.A. / Seo Lee, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Davis, B.G. / Yue, W.W.
CitationJournal: Nature / Year: 2018
Title: Palladium-mediated enzyme activation suggests multiphase initiation of glycogenesis.
Authors: Bilyard, M.K. / Bailey, H.J. / Raich, L. / Gafitescu, M.A. / Machida, T. / Iglesias-Fernandez, J. / Lee, S.S. / Spicer, C.D. / Rovira, C. / Yue, W.W. / Davis, B.G.
History
DepositionOct 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 14, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0326
Polymers29,7221
Non-polymers3105
Water75742
1
A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,06412
Polymers59,4432
Non-polymers62110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3960 Å2
ΔGint3 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.030, 101.020, 49.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glycogenin-1 / GN1


Mass: 29721.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GYG1, GYG / Production host: Escherichia coli (E. coli) / References: UniProt: P46976, glycogenin glucosyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 28% PEG smear broad, 0.1M sodium/potassium phosphate pH 6.2, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.18→101.02 Å / Num. obs: 15830 / % possible obs: 98.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 46.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.033 / Rrim(I) all: 0.081 / Net I/σ(I): 12.6 / Num. measured all: 88786 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.18-2.242.80.77110420.6640.510.93389.6
9.75-101.0250.0372250.9980.0180.04299.7

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
MOLREPphasing
RefinementResolution: 2.18→50.967 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.78
RfactorNum. reflection% reflection
Rfree0.2604 777 4.92 %
Rwork0.2288 --
obs0.2304 15792 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.81 Å2 / Biso mean: 51.5879 Å2 / Biso min: 33.15 Å2
Refinement stepCycle: final / Resolution: 2.18→50.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 20 42 1956
Biso mean--63.53 51.98 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011958
X-RAY DIFFRACTIONf_angle_d0.3872668
X-RAY DIFFRACTIONf_chiral_restr0.04313
X-RAY DIFFRACTIONf_plane_restr0.004334
X-RAY DIFFRACTIONf_dihedral_angle_d9.0631131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1801-2.31670.37761320.34572282241493
2.3167-2.49560.35531190.27862497261699
2.4956-2.74670.32041310.265425012632100
2.7467-3.14410.30271400.277224942634100
3.1441-3.9610.25381280.230625482676100
3.961-50.98040.20821270.186726932820100

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