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- PDB-1zdf: Ser162 mutant of glycogenin complexed with UDP-glucose and manganese -

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Basic information

Entry
Database: PDB / ID: 1zdf
TitleSer162 mutant of glycogenin complexed with UDP-glucose and manganese
ComponentsGlycogenin-1
KeywordsTRANSFERASE / glycosyltransferase
Function / homology
Function and homology information


glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity
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-GLUCOSE / Glycogenin-1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHurley, T.D. / Stout, S.L. / Miner, E. / Zhou, J. / Roach, P.J.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Requirements for catalysis in mammalian glycogenin.
Authors: Hurley, T.D. / Stout, S. / Miner, E. / Zhou, J. / Roach, P.J.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: The structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin
Authors: Gibbons, B.J. / Roach, P.J. / Hurley, T.D.
History
DepositionApr 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Oct 20, 2021Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)40,2934
Polymers39,5761
Non-polymers7173
Water1,820101
1
A: Glycogenin-1
hetero molecules

A: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5878
Polymers79,1522
Non-polymers1,4356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area4510 Å2
ΔGint-53 kcal/mol
Surface area21440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.890, 105.380, 122.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

21A-450-

HOH

31A-504-

HOH

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Components

#1: Protein Glycogenin-1 /


Mass: 39576.195 Da / Num. of mol.: 1 / Mutation: D162S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: GYG, GYG1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL 21 / References: UniProt: P13280, 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.4 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: sodium MES, ammonium sulfate, PEG MME 5000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2003
RadiationMonochromator: osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→33 Å / Num. all: 14347 / Num. obs: 14237 / % possible obs: 99.4 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 5.9 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.038 / Net I/σ(I): 21.7
Reflection shellResolution: 2.45→2.54 Å / % possible obs: 93.8 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.6 / Num. measured obs: 1312 / Χ2: 1.034 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.6data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LL3

1ll3


Resolution: 2.45→33 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 706 4.9 %random
Rwork0.199 ---
all0.251 14349 --
obs0.2 14072 98.1 %-
Solvent computationBsol: 20.612 Å2
Displacement parametersBiso mean: 40.575 Å2
Baniso -1Baniso -2Baniso -3
1--16.612 Å20 Å20 Å2
2--5.079 Å20 Å2
3---11.533 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.45→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 39 101 2189
Refine LS restraints
Refine-IDTypeDev idealWeightDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4791.5
X-RAY DIFFRACTIONc_scbond_it2.15720
X-RAY DIFFRACTIONc_mcangle_it2.52920
X-RAY DIFFRACTIONc_scangle_it3.252.50
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.61
X-RAY DIFFRACTIONc_improper_angle_d1.14
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3water.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5upg.param

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