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- PDB-1qkj: T4 Phage B-Glucosyltransferase, Substrate Binding and Proposed Ca... -

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Basic information

Entry
Database: PDB / ID: 1qkj
TitleT4 Phage B-Glucosyltransferase, Substrate Binding and Proposed Catalytic Mechanism
ComponentsBETA-GLUCOSYLTRANSFERASE
KeywordsTRANSFERASE (GLUCOSYLTRANSFERASE) / TRANSFERASE(GLUCOSYLTRANSFERASE)
Function / homology
Function and homology information


DNA beta-glucosyltransferase / DNA beta-glucosyltransferase activity / symbiont-mediated evasion of host restriction-modification system / DNA modification
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 speciesBACTERIOPHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMorera, S. / Imberty, I. / 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. / Rueger, W. / Driessen, H.P.C. / Freemont, P.S.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Studies of T4 Phage Beta-Glucosyltransferase
Authors: Freemont, P.S. / Rueger, W.
#3: Journal: Nucleic Acids Res. / Year: 1985
Title: T4-Induced Alpha- and Beta-Glucosyltransferase: Cloning of the Genes and a Comparison of Their Products Based on Sequencing Data
Authors: Tomaschewski, J. / Gram, H. / Crabb, J.W. / Ruger, W.
History
DepositionJul 22, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / struct
Item: _citation.page_last / _diffrn_source.pdbx_synchrotron_beamline ..._citation.page_last / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _struct.title
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: BETA-GLUCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1242
Polymers40,7201
Non-polymers4041
Water2,414134
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.460, 102.470, 59.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL_UNIT: MONOMER

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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.) BACTERIOPHAGE T4 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04547, DNA beta-glucosyltransferase
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBETA-GLUCOSYLTRANSFERASE TRANSFERS A BETA-D-GLUCOSYL RESIDUE FROM UDP-GLUCOSE TO AN ...BETA-GLUCOSYLTRANSFERASE TRANSFERS A BETA-D-GLUCOSYL RESIDUE FROM UDP-GLUCOSE TO AN HYDROXYMETHYLCYTOSINE RESIDUE IN DNA. INVOLVED IN THE DNA MODIFICATION PROCESS TO PROTECTS THE PHAGE GENOME AGAINS ITS OWN NUCLEASES AND THE HOST RESTRICTION ENDONUCLEASE SYSTEM.

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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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growpH: 7.4 / Details: pH 7.40
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %(w/v)PEG40001drop
250 mMTris-HCl1drop
31 mMprotein1drop
420 %(w/v)PEG40001reservoir
552 %satammonium sulfate1reservoir
60.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 16930 / % possible obs: 96 % / Redundancy: 5 % / Rsym value: 0.41
Reflection
*PLUS
Num. measured all: 57848 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 78 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
X-PLOR3.84refinement
X-PLOR3.84phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BGU

1bgu


Resolution: 2.3→20 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.29 -10 %RANDOM
Rwork0.19 ---
obs0.19 86 96 %-
Displacement parametersBiso mean: 17.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 25 134 3028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.822
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_d1.682
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
Version: 3.84 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16489 / Rfactor obs: 0.198 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.682

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