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- PDB-1y6f: alpha-glucosyltransferase in complex with UDP-glucose and DNA con... -

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Basic information

Entry
Database: PDB / ID: 1y6f
Titlealpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site
Components
  • 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
  • 5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3'
  • DNA alpha-glucosyltransferase
KeywordsTRANSFERASE/DNA / Transferase / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA alpha-glucosyltransferase / DNA alpha-glucosyltransferase activity / symbiont-mediated suppression of host CRISPR-cas system / symbiont-mediated evasion of host restriction-modification system / DNA modification
Similarity search - Function
DNA alpha-glucosyltransferase / DNA alpha-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / DNA / DNA (> 10) / DNA alpha-glucosyltransferase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLariviere, L. / Sommer, N. / Morera, S.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.
Authors: Lariviere, L. / Sommer, N. / Morera, S.
History
DepositionDec 6, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3'
D: 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
A: DNA alpha-glucosyltransferase
B: DNA alpha-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,46612
Polymers101,9154
Non-polymers1,5518
Water4,035224
1
C: 5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3'
A: DNA alpha-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7896
Polymers50,9322
Non-polymers8574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
B: DNA alpha-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6776
Polymers50,9832
Non-polymers6944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.363, 123.964, 86.628
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules CD

#1: DNA chain 5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3'


Mass: 3890.550 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'


Mass: 3941.584 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein DNA alpha-glucosyltransferase / / AGT


Mass: 47041.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Plasmid: proExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): XL1blue / References: UniProt: P04519, DNA alpha-glucosyltransferase

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Non-polymers , 5 types, 232 molecules

#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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2H2O11
3PEG 400012
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2004
RadiationMonochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 38189 / Num. obs: 37879 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rsym value: 0.082 / Net I/σ(I): 12.9
Reflection shellResolution: 2.4→2.49 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a model at 2.7 A from a SAD experiment (selenomethionines)

Resolution: 2.4→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 1888 random
Rwork0.197 --
all-37879 -
obs-37879 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6469 519 99 224 7311
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.31
X-RAY DIFFRACTIONc_angle_d0.007

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