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- PDB-1c3j: T4 PHAGE BETA-GLUCOSYLTRANSFERASE: SUBSTRATE BINDING AND PROPOSED... -

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Basic information

Entry
Database: PDB / ID: 1c3j
TitleT4 PHAGE BETA-GLUCOSYLTRANSFERASE: SUBSTRATE BINDING AND PROPOSED CATALYTIC MECHANISM
ComponentsBETA-GLUCOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


DNA beta-glucosyltransferase / DNA beta-glucosyltransferase activity / symbiont-mediated evasion of host restriction-modification system / DNA modification / symbiont-mediated suppression of host innate immune 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
URIDINE-5'-DIPHOSPHATE / DNA beta-glucosyltransferase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.88 Å
AuthorsMorera, S. / Imberty, A. / Aschke-Sonnenborn, U. / Ruger, W. / Freemont, P.S.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism.
Authors: Morera, S. / Imberty, A. / Aschke-Sonnenborn, U. / Ruger, W. / Freemont, P.S.
#1: Journal: Embo J. / Year: 1994
Title: Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
Authors: Vrielink, A. / Ruger, W. / Driessen, H.P.C. / Freemont, P.
History
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 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

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Assembly

Deposited unit
A: BETA-GLUCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1242
Polymers40,7201
Non-polymers4041
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.700, 52.260, 52.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BETA-GLUCOSYLTRANSFERASE


Mass: 40719.879 Da / Num. of mol.: 1
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P04547, DNA beta-glucosyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 51.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: AMMONIUM SULFATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
PH range low: 5.8 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
226 %satammonium sulfate1drop
31 mMUDP1drop
452 %satammonium sulfate1reservoir
50.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.88→26 Å / Num. all: 223460 / Num. obs: 31888 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 19.659 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 3 % / Rmerge(I) obs: 0.278 / % possible all: 71
Reflection
*PLUS
Num. measured all: 223460
Reflection shell
*PLUS
% possible obs: 71 %

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Processing

Software
NameVersionClassification
FFTmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing
RefinementResolution: 1.88→20 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3129 -RANDOM
Rwork0.191 ---
all0.191 31888 --
obs0.191 31297 82 %-
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 25 166 2908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.788
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.606
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.67 Å2

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