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- PDB-3t7o: Crystal Structure of Human Glycogenin-1 (GYG1) complexed with man... -

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Basic information

Entry
Database: PDB / ID: 3t7o
TitleCrystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP-Glucose and glucose
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 synthesis ...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 / 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
alpha-D-glucopyranose / : / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glycogenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionJul 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,82526
Polymers59,2232
Non-polymers2,60224
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-23 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.415, 46.590, 69.904
Angle α, β, γ (deg.)79.54, 88.75, 75.83
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 3 molecules AB

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


Mass: 29611.639 Da / Num. of mol.: 2 / Fragment: glycogenin (UNP 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: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 545 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0M Ammonium Sulphate, 0.1M Bis-Tris, pH 6.5, 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: Dec 20, 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: 1.85→30.4 Å / Num. all: 44258 / Num. obs: 44222 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6135 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q4S

3q4s


Resolution: 1.85→28.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.999 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25501 2217 5 %RANDOM
Rwork0.19506 ---
obs0.19809 42005 92.84 %-
all-44222 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.652 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å2-1.66 Å20.83 Å2
2--0.28 Å20.99 Å2
3----1.09 Å2
Refine analyzeLuzzati coordinate error obs: 0.237 Å
Refinement stepCycle: LAST / Resolution: 1.85→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 162 522 4853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224472
X-RAY DIFFRACTIONr_bond_other_d0.0010.022968
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9786067
X-RAY DIFFRACTIONr_angle_other_deg1.07437243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43524.043188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92415696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.51518
X-RAY DIFFRACTIONr_chiral_restr0.120.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
X-RAY DIFFRACTIONr_mcbond_it0.6411.52647
X-RAY DIFFRACTIONr_mcbond_other0.1861.51053
X-RAY DIFFRACTIONr_mcangle_it1.0924315
X-RAY DIFFRACTIONr_scbond_it1.91631825
X-RAY DIFFRACTIONr_scangle_it2.7464.51747
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 158 -
Rwork0.303 2895 -
obs--87.83 %
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)
11.33130.4499-0.42531.52110.31352.9165-0.0149-0.059-0.0346-0.0395-0.00280.0183-0.14690.09090.01770.04150.003400.00810.01190.046631.992325.318221.1028
23.07430.69940.40786.07061.55636.3325-0.1201-0.139-0.190.2889-0.0316-0.14720.40970.17070.15160.10640.02660.01610.0150.00340.150733.43645.636316.4237
31.60320.30440.41740.8454-0.50932.3925-0.01430.0292-0.0299-0.02520.0001-0.04280.0806-0.06040.01420.03720.00510.02080.0291-0.0080.033822.83315.532552.6499
44.61960.0684-2.48124.4664-1.609111.6697-0.04990.02970.1354-0.1182-0.04450.0620.31860.39020.09430.01940.0216-0.02680.08350.00170.108338.562712.825159.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 212
2X-RAY DIFFRACTION2A213 - 262
3X-RAY DIFFRACTION3B0 - 236
4X-RAY DIFFRACTION4B237 - 262

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