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

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Basic information

Entry
Database: PDB / ID: 6eql
TitleCrystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant complexed with manganese and UDP
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
: / URIDINE-5'-DIPHOSPHATE / Glycogenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.38 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogenin-1
B: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8388
Polymers59,4432
Non-polymers1,3956
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-44 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.170, 81.050, 111.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycogenin-1 / GN1


Mass: 29721.533 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 47 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 22.5% PEG Smear High, 0.2M potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.38→46.55 Å / Num. obs: 24661 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 47.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.068 / Rrim(I) all: 0.173 / Net I/σ(I): 9.2 / Num. measured all: 159048 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.38-2.446.71.73117990.5120.7181.87699.8
10.64-46.555.20.0293310.9990.0140.03299.1

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 2.38→46.55 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9
RfactorNum. reflection% reflection
Rfree0.2807 1209 4.91 %
Rwork0.2253 --
obs0.228 24603 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.31 Å2 / Biso mean: 52.0824 Å2 / Biso min: 29.71 Å2
Refinement stepCycle: final / Resolution: 2.38→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 84 41 3840
Biso mean--54.01 48.04 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063908
X-RAY DIFFRACTIONf_angle_d0.445323
X-RAY DIFFRACTIONf_chiral_restr0.041621
X-RAY DIFFRACTIONf_plane_restr0.004656
X-RAY DIFFRACTIONf_dihedral_angle_d7.5162677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3801-2.47540.36271240.320825492673
2.4754-2.5880.35471510.314525512702
2.588-2.72450.35121230.300425482671
2.7245-2.89510.34011330.268925812714
2.8951-3.11860.31461230.262425932716
3.1186-3.43240.28191370.233825692706
3.4324-3.92880.27761300.215726202750
3.9288-4.9490.22991650.179325982763
4.949-46.55890.27161230.203927852908

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