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- PDB-1nzf: T4 phage BGT-D100A mutant in complex with UDP-glucose: Form II -

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Basic information

Entry
Database: PDB / ID: 1nzf
TitleT4 phage BGT-D100A mutant in complex with UDP-glucose: Form II
ComponentsDNA beta-glycosyltransferase
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
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: 2.1 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
DepositionFeb 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA beta-glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4976
Polymers40,6761
Non-polymers8215
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.119, 72.958, 80.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA beta-glycosyltransferase / BGT


Mass: 40675.871 Da / Num. of mol.: 1 / Mutation: D100A
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.02 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: peg 4000, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2003
RadiationMonochromator: 0.95 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 22179 / Num. obs: 21948 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28 Å2 / Rsym value: 0.05 / Net I/σ(I): 18.7
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 5.5 / Num. unique all: 2146 / Rsym value: 0.3 / % possible all: 99

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J39

1j39


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.22 1072 random
Rwork0.183 --
all-22179 -
obs-21948 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.967 Å20 Å20 Å2
2---1.722 Å20 Å2
3---2.688 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 50 337 3254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.23
X-RAY DIFFRACTIONc_mcbond_it1.2341.5
X-RAY DIFFRACTIONc_scbond_it2.1822
X-RAY DIFFRACTIONc_mcangle_it1.8892
X-RAY DIFFRACTIONc_scangle_it3.0942.5
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
X-RAY DIFFRACTION5gol.paramgol.top

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