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- PDB-3u2t: Crystal Structure of Human Glycogenin-1 (GYG1) complexed with man... -

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Basic information

Entry
Database: PDB / ID: 3u2t
TitleCrystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese
ComponentsGlycogenin-1
KeywordsTRANSFERASE / Structural Genomics / 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) / 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 / 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: 2.05 Å
AuthorsChaikuad, A. / Froese, D.S. / Krysztofinska, E. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Yue, W.W. / 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
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3876
Polymers32,0831
Non-polymers3035
Water2,522140
1
A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,77312
Polymers64,1672
Non-polymers60610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3340 Å2
ΔGint-24 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.350, 101.060, 47.830
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-400-

HOH

DetailsThe other subunit in the dimer pair is generated by the two fold axis: -x,-y,z

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Components

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


Mass: 32083.301 Da / Num. of mol.: 1 / Fragment: glycogenin (residues 1-262)
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22.5% PEG smears, 0.2M Li2(SO4), 0.05M ZnCl2, 0.1M Bis-Tris, pH 7.5, 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: Oct 22, 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: 2.05→38.2 Å / Num. all: 18360 / Num. obs: 18330 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 10
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2636 / % possible all: 99.2

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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 ENTRY 3Q4S

3q4s


Resolution: 2.05→36.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.006 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25114 940 5.1 %RANDOM
Rwork0.19902 ---
obs0.20144 17417 99.58 %-
all-18360 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.638 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---2.41 Å20 Å2
3---2.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: LAST / Resolution: 2.05→36.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 17 140 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222093
X-RAY DIFFRACTIONr_bond_other_d0.0040.021383
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9532845
X-RAY DIFFRACTIONr_angle_other_deg1.05833384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11224.38289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28615339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.112158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
X-RAY DIFFRACTIONr_mcbond_it0.5561.51286
X-RAY DIFFRACTIONr_mcbond_other0.1241.5514
X-RAY DIFFRACTIONr_mcangle_it1.01122089
X-RAY DIFFRACTIONr_scbond_it1.6693807
X-RAY DIFFRACTIONr_scangle_it2.4954.5753
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 81 -
Rwork0.314 1247 -
obs--98.52 %
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)
12.2461-0.07670.32332.1929-0.40161.51930.01890.0514-0.0106-0.1257-0.0040.07750.0112-0.0331-0.01490.0340.00980.00230.0099-0.00370.011318.026614.915311.2567
213.5866-9.09231.07419.90930.50787.89230.1110.176-0.8154-0.7604-0.03251.20980.0525-0.4543-0.07850.1651-0.0686-0.08610.1633-0.02570.11684.64048.5414-0.3722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 233
2X-RAY DIFFRACTION2A240 - 262

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