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- PDB-3q4s: Crystal Structure of Human Glycogenin-1 (GYG1), apo form -

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Basic information

Entry
Database: PDB / ID: 3q4s
TitleCrystal Structure of Human Glycogenin-1 (GYG1), apo form
ComponentsGlycogenin-1
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / glycosyltransferase / glycogen biosynthesis / glycosylation
Function / homology
Function and homology information


Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogenin glucosyltransferase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase activity / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis ...Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogenin glucosyltransferase / Glycogen storage disease type II (GAA) / 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 / nucleus / membrane / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsChaikuad, A. / Froese, D.S. / Yue, W.W. / Krysztofinska, E. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, O. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis.
Authors: Chaikuad, A. / Froese, D.S. / Berridge, G. / von Delft, F. / Oppermann, U. / Yue, W.W.
History
DepositionDec 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Jan 11, 2012Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)30,19011
Polymers29,5961
Non-polymers59410
Water4,360242
1
A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,37922
Polymers59,1912
Non-polymers1,18820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5900 Å2
ΔGint12 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.020, 101.220, 48.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-272-

CL

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Components

#1: Protein Glycogenin-1 / GN-1 / GN1


Mass: 29595.639 Da / Num. of mol.: 1 / Fragment: glycogenin (residues 1-262) / Mutation: Y195F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GYG, GYG1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P46976, glycogenin glucosyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG smears (PEG 2000, 3350, 4000, 5000MME), 0.1M PIPES, pH 7.0, 0.1M MgCl2, 0.1M KCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 4, 2010
RadiationMonochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→30.04 Å / Num. all: 19979 / Num. obs: 19954 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.2
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2 / Num. unique all: 2784 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1LL3

1ll3


Resolution: 1.98→29.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.12 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IN REFINEMENT BUT NOT OUTPUT TO PDB
RfactorNum. reflection% reflectionSelection details
Rfree0.23827 1017 5.1 %RANDOM
Rwork0.17844 ---
obs0.18146 18959 96.52 %-
all-19954 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.295 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---1.41 Å20 Å2
3---2.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: LAST / Resolution: 1.98→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 37 242 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222068
X-RAY DIFFRACTIONr_bond_other_d0.0010.021380
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9572799
X-RAY DIFFRACTIONr_angle_other_deg1.01333368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69324.36887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34415329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.208157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_mcbond_it1.71631256
X-RAY DIFFRACTIONr_mcbond_other0.4613502
X-RAY DIFFRACTIONr_mcangle_it2.67652041
X-RAY DIFFRACTIONr_scbond_it4.3568812
X-RAY DIFFRACTIONr_scangle_it5.92511757
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 73 -
Rwork0.304 1341 -
obs--93.89 %
Refinement TLS params.

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

IDL11 (°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)
11.536-0.09450.31631.8932-0.24221.0732-0.0319-0.11710.07710.09880.05140.011-0.0464-0.0439-0.01960.05370.01470.0180.0288-0.01330.020519.073117.438613.833
20.18490.7122-0.248616.93311.01080.6439-0.1387-0.0765-0.1304-0.61620.033-0.18650.23240.19920.10560.29110.0692-0.11750.2193-0.04620.449217.6604-3.59736.5132
34.48270.19561.66044.80770.76626.1180.0350.1931-0.2291-0.3734-0.00560.14010.1364-0.189-0.02940.1625-0.0032-0.02520.1193-0.02160.166.57968.814-3.7731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 191
2X-RAY DIFFRACTION2A192 - 213
3X-RAY DIFFRACTION3A214 - 262

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