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- PDB-1zct: structure of glycogenin truncated at residue 270 in a complex with UDP -

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Basic information

Entry
Database: PDB / ID: 1zct
Titlestructure of glycogenin truncated at residue 270 in a complex with UDP
ComponentsGlycogenin-1
KeywordsTRANSFERASE / glycosyltransferase
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
: / URIDINE-5'-DIPHOSPHATE / Glycogenin-1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin
Authors: Gibbons, B.J. / Roach, P.J. / Hurley, T.D.
History
DepositionApr 13, 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: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_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

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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)65,9276
Polymers65,0092
Non-polymers9184
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-53 kcal/mol
Surface area22220 Å2
MethodPISA
2
A: Glycogenin-1
B: Glycogenin-1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)131,85512
Polymers130,0184
Non-polymers1,8368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area12040 Å2
ΔGint-122 kcal/mol
Surface area40400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.000, 75.000, 233.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Glycogenin-1


Mass: 32504.529 Da / Num. of mol.: 2
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(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13280, glycogenin glucosyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, PEG 4000, uridine-diphosphoglucose, manganese chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2003
RadiationMonochromator: APS 17ID design / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 22737 / Num. obs: 20872 / % possible obs: 91.2 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 10.1 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.054 / Net I/σ(I): 28.2
Reflection shellResolution: 2.6→2.69 Å / % possible obs: 53.8 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 7.4 / Num. measured obs: 1224 / Χ2: 1.062 / % possible all: 53.8

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Phasing

Phasing MRRfactor: 43.5 / Cor.coef. Fo:Fc: 60.1 / Cor.coef. Io to Ic: 54.6
Highest resolutionLowest resolution
Rotation4 Å35 Å
Translation4 Å25 Å

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Processing

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

1ll3


Resolution: 2.6→20 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1067 4.7 %random
Rwork0.239 ---
all0.28 22737 --
obs0.24 20738 91.2 %-
Solvent computationBsol: 31.617 Å2
Displacement parametersBiso mean: 74.231 Å2
Baniso -1Baniso -2Baniso -3
1--22.847 Å2-14.45 Å20 Å2
2---22.847 Å20 Å2
3---45.694 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 52 55 4195
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.3850
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_mcangle_it1.66
X-RAY DIFFRACTIONc_mcbond_it2.91
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3udp.param
X-RAY DIFFRACTION4cis_peptide.param
X-RAY DIFFRACTION5water.param

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