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- PDB-1jix: T4 Phage BGT in Complex with Ca2+ -

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Basic information

Entry
Database: PDB / ID: 1jix
TitleT4 Phage BGT in Complex with Ca2+
ComponentsDNA BETA-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMorera, S. / Lariviere, L. / Kurzeck, J. / Aschke-Sonnenborn, U. / Freemont, P.S. / Janin, J. / Ruger, W.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: High resolution crystal structures of T4 phage beta-glucosyltransferase: induced fit and effect of substrate and metal binding.
Authors: Morera, S. / Lariviere, L. / Kurzeck, J. / Aschke-Sonnenborn, U. / Freemont, P.S. / Janin, J. / Ruger, W.
#1: 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.
History
DepositionJul 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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)41,1643
Polymers40,7201
Non-polymers4442
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.943, 71.454, 62.010
Angle α, β, γ (deg.)90.00, 91.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P04547, DNA beta-glucosyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-11 %PEG40001drop
2100 mMTris-HCl1droppH7.5
31 mMUDP1drop
420-22 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 50720 / Num. obs: 49706 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 6.5 / Num. unique all: 4908 / % possible all: 97.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 304335 / Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QKJ

1qkj


Resolution: 1.65→20 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2477 -RANDOM
Rwork0.2 ---
all-50320 --
obs-49706 98.8 %-
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 26 436 3357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.23
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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