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- PDB-1sxp: BGT in complex with a 13mer DNA containing a central A:G mismatch -

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Basic information

Entry
Database: PDB / ID: 1sxp
TitleBGT in complex with a 13mer DNA containing a central A:G mismatch
Components
  • 5'-D(*A*AP*TP*AP*CP*TP*AP*AP*GP*AP*TP*AP*G)-3'
  • 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*T)-3'
  • DNA beta-glucosyltransferase
KeywordsTRANSFERASE/DNA / flipped-out base / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA beta-glucosyltransferase / DNA beta-glucosyltransferase activity / symbiont-mediated evasion of host restriction-modification system / DNA modification / virus-mediated perturbation of host defense response
Similarity search - Function
DNA beta-glucosyltransferase, bacteriophage / Bacteriophage T4 beta-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA beta-glucosyltransferase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLariviere, L. / Morera, S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural evidence of a passive base flipping mechanism for {beta}-Glucosyltransferase
Authors: Lariviere, L. / Morera, S.
History
DepositionMar 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 22, 2020Group: Advisory / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _ndb_struct_na_base_pair.propeller
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: 5'-D(*A*AP*TP*AP*CP*TP*AP*AP*GP*AP*TP*AP*G)-3'
D: 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*T)-3'
A: DNA beta-glucosyltransferase
B: DNA beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8768
Polymers89,4054
Non-polymers4714
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-11 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.354, 172.821, 60.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 2 molecules CD

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


Mass: 4023.661 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*T)-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 beta-glucosyltransferase / BGT


Mass: 40719.879 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 / Gene: BGT, BETA-GT / Production host: Escherichia coli (E. coli) / References: UniProt: P04547, DNA beta-glucosyltransferase

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Non-polymers , 3 types, 243 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.56 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutionsName: PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 8, 2003
RadiationMonochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 32619 / Num. obs: 31422 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.075
Reflection shellResolution: 2.5→2.63 Å / Rsym value: 0.34 / % possible all: 94.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 1555 random
Rwork0.212 --
all-32619 -
obs-31395 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5740 488 31 239 6498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00667
X-RAY DIFFRACTIONc_angle_d1.24

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