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- PDB-2bgu: CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME BETA-GLUCOSYLTRANSF... -

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Basic information

Entry
Database: PDB / ID: 2bgu
TitleCRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME BETA-GLUCOSYLTRANSFERASE IN THE PRESENCE AND ABSENCE OF THE SUBSTRATE URIDINE DIPHOSPHOGLUCOSE
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
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 / Resolution: 2.2 Å
AuthorsVrielink, A. / Rueger, W. / Driessen, H.P.C. / Freemont, P.S.
Citation
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. / Freemont, P.S.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Studies of T4 Phage Beta-Glucosyltransferase
Authors: Freemont, P.S. / Ruger, W.
#2: 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
DepositionJun 9, 1994Processing site: BNL
Revision 1.0Dec 9, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.920, 52.260, 52.740
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 / 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.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / 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
30.05 mMUDPG1drop
40.05 Msodium citrate1drop
526 %satammonium sulfate1reservoir
60.1 mMUDPG1reservoir
70.1 Msodium citrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 21380 / % possible obs: 94.5 % / Num. measured all: 74613 / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 0
Details: THE COORDINATES ARE PRESENTED IN A COORDINATE FRAME THAT IS TRANSLATED BY 1/4*151.920 ALONG A AND 1/4*52.26 ALONG B. THUS THE TRANSFORMATION PRESENTED ON *SCALE* RECORDS BELOW IS NOT THE ...Details: THE COORDINATES ARE PRESENTED IN A COORDINATE FRAME THAT IS TRANSLATED BY 1/4*151.920 ALONG A AND 1/4*52.26 ALONG B. THUS THE TRANSFORMATION PRESENTED ON *SCALE* RECORDS BELOW IS NOT THE DEFAULT. THE DICTIONARY FOR THE UDP PORTION OF THE SUBSTRATE WAS BUILT USING THE CHARM MINIMIZATION WITHIN QUANTA.
RfactorNum. reflection
Rwork0.191 -
obs0.191 20885
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 25 221 2918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg
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 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21 Å2

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