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- PDB-1ixy: Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex -

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Basic information

Entry
Database: PDB / ID: 1ixy
TitleTernary complex of T4 phage BGT with UDP and a 13 mer DNA duplex
Components
  • 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
  • 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'
  • DNA beta-glucosyltransferase
KeywordsTRANSFERASE/DNA / protein-dna complex / base-flipping / abasic site / TRANSFERASE-DNA COMPLEX
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 / DNA (> 10) / DNA beta-glucosyltransferase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLariviere, L. / Morera, S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: A Base-flipping Mechanism for the T4 Phage beta-Glucosyltransferase and Identification of a Transition-state Analog
Authors: Lariviere, L. / Morera, S.
History
DepositionJul 9, 2002Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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
C: 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'
E: 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
D: 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'
F: 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
A: DNA beta-glucosyltransferase
B: DNA beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,34014
Polymers97,1046
Non-polymers1,2368
Water4,324240
1
C: 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'
E: 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
A: DNA beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2177
Polymers48,5523
Non-polymers6654
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'
F: 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
B: DNA beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1237
Polymers48,5523
Non-polymers5714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.9, 56.4, 99.1
Angle α, β, γ (deg.)90, 90.3, 90
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules CDEF

#1: DNA chain 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'


Mass: 3890.550 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'


Mass: 3941.584 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein DNA beta-glucosyltransferase / / BGT


Mass: 40719.879 Da / Num. of mol.: 2
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): BL21(DE3) / References: UniProt: P04547, DNA beta-glucosyltransferase

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Non-polymers , 4 types, 248 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, tert-butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2tert-butanol11
3MPD12
Crystal grow
*PLUS
Details: Lariviere, L., (2002) Acta Crystallogr., Sect.D, 58, 1484.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMDNA1drop
250 mMBGT1drop
30.5 mMUDP-glucose1drop
422 %MPD1drop
52 %t-butanol1drop
644 %MPD1reservoir
74 %t-butanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 30519 / Num. obs: 30397 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 54.2 Å2 / Rsym value: 0.102 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.63 Å / Mean I/σ(I) obs: 2.26 / Num. unique all: 4374 / Rsym value: 0.499 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.102

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1JG6

1jg6


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1507 -RANDOM
Rwork0.209 ---
all-30519 --
obs-30397 99.6 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5738 1038 53 264 7093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00672
X-RAY DIFFRACTIONc_angle_deg1.21
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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