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- PDB-3v8y: Structure of apo-glycogenin truncated at residue 270 -

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Basic information

Entry
Database: PDB / ID: 3v8y
TitleStructure of apo-glycogenin truncated at residue 270
ComponentsGlycogenin-1
KeywordsTRANSFERASE
Function / homology
Function and homology information


glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity / nucleus / 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 speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsCarrizo, M.E. / Romero, J.M. / Issoglio, F.M. / Curtino, J.A.
CitationJournal: Febs Lett. / Year: 2012
Title: Structural and biochemical insight into glycogenin inactivation by the glycogenosis-causing T82M mutation.
Authors: Carrizo, M.E. / Romero, J.M. / Issoglio, F.M. / Curtino, J.A.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)32,8274
Polymers32,6081
Non-polymers2203
Water1,76598
1
A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6558
Polymers65,2152
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area3390 Å2
ΔGint-25 kcal/mol
Surface area21260 Å2
MethodPISA
2
A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,30916
Polymers130,4314
Non-polymers87912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_546x,-y-1,-z+11
Buried area10540 Å2
ΔGint-198 kcal/mol
Surface area39250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.630, 104.220, 120.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 32607.670 Da / Num. of mol.: 1 / Fragment: UNP residues 1-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: GYG, GYG1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): CGSC 4997 / References: UniProt: P13280, glycogenin glucosyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 98 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.0 M ammonium sulate/0.1M sodium phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 18, 2010 / Details: mirrors
RadiationMonochromator: Silicium curved crystal, with asymmetric 7.25 angle cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 2.15→27.82 Å / Num. all: 20120 / Num. obs: 20120 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2885 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.15→27.82 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.128 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23887 1023 5.1 %RANDOM
Rwork0.20556 ---
obs0.20719 19061 99.69 %-
all-19061 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.368 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2---0.45 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.15→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 13 98 2166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222118
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9442884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79624.25594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53315337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.893158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211590
X-RAY DIFFRACTIONr_mcbond_it0.7681.51291
X-RAY DIFFRACTIONr_mcangle_it1.45322097
X-RAY DIFFRACTIONr_scbond_it1.9763827
X-RAY DIFFRACTIONr_scangle_it3.2144.5787
LS refinement shellResolution: 2.149→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 70 -
Rwork0.262 1391 -
obs--99.05 %

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