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- PDB-1j39: Crystal Structure of T4 phage BGT in complex with its UDP-glucose... -

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Basic information

Entry
Database: PDB / ID: 1j39
TitleCrystal Structure of T4 phage BGT in complex with its UDP-glucose substrate
ComponentsDNA beta-glucosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / GT-B / UDP-glucose
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-GLUCOSE / DNA beta-glucosyltransferase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLariviere, L. / Morera, S.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structures of the T4 phage beta-glucosyltransferase and the D100A mutant in complex with UDP-glucose: glucose binding and identification of the catalytic base for a direct displacement mechanism.
Authors: Lariviere, L. / Gueguen-Chaignon, V. / Morera, S.
History
DepositionJan 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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 / 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: DNA beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5625
Polymers40,7201
Non-polymers8434
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.391, 51.431, 52.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-691-

HOH

21A-784-

HOH

DetailsThe biological assembly is a monomer

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Components

#1: Protein DNA beta-glucosyltransferase / T4 phage beta-glucosyltransferase / BGT


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 / Gene: BGT / Plasmid: pBSK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P04547, DNA beta-glucosyltransferase
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.29 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.8 Mammonium sulfate1drop
250 mMTris-HCl1droppH8.5
31.6 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.87→20 Å / Num. all: 34553 / Num. obs: 34069 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.047 / Net I/σ(I): 11.3
Reflection shellResolution: 1.87→1.94 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 3391 / Rsym value: 0.239 / % possible all: 96.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 34078 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.239

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BGT

2bgt


Resolution: 1.87→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1689 -RANDOM
Rwork0.194 ---
all-34553 --
obs-34069 98.6 %-
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.753 Å20 Å20 Å2
2---5.866 Å20 Å2
3---3.113 Å2
Refinement stepCycle: LAST / Resolution: 1.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 54 328 3169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00515
X-RAY DIFFRACTIONc_angle_deg1.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4upg.paramupg.top
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2

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