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- PDB-6hn7: Hijacking the Hijackers: Escherichia coli Pathogenicity Islands R... -

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Basic information

Entry
Database: PDB / ID: 6hn7
TitleHijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit.
Components
  • Redirecting phage packaging protein C (RppC)
  • Terminase small subunit
KeywordsDNA BINDING PROTEIN / Redirecting packaging protein / Hetero-dimer / phage interference / Protein complex
Function / homology
Function and homology information


viral terminase, small subunit / sequence-specific DNA binding, bending / viral DNA genome packaging / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / ATP hydrolysis activity / ATP binding
Similarity search - Function
Bacteriophage lambda, Nu1, terminase small subunit / Phage DNA packaging protein Nu1 / Putative DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Redirecting phage packaging protein C (RppC) / Terminase small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia virus Lambda
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPenades, J.R. / Bacarizo, J. / Marina, A. / Alqasmi, M. / Fillol-Salom, A. / Roszak, A.W. / Ciges-Tomas, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council670932 United Kingdom
CitationJournal: Mol.Cell / Year: 2019
Title: Hijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit.
Authors: Fillol-Salom, A. / Bacarizo, J. / Alqasmi, M. / Ciges-Tomas, J.R. / Martinez-Rubio, R. / Roszak, A.W. / Cogdell, R.J. / Chen, J. / Marina, A. / Penades, J.R.
History
DepositionSep 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Redirecting phage packaging protein C (RppC)
B: Terminase small subunit


Theoretical massNumber of molelcules
Total (without water)29,3012
Polymers29,3012
Non-polymers00
Water36020
1
A: Redirecting phage packaging protein C (RppC)
B: Terminase small subunit

A: Redirecting phage packaging protein C (RppC)
B: Terminase small subunit


Theoretical massNumber of molelcules
Total (without water)58,6024
Polymers58,6024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7620 Å2
ΔGint-48 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.523, 101.004, 82.627
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Redirecting phage packaging protein C (RppC)


Mass: 17828.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CXXR01000010.1 / Variant: EC2733.1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5H1ZR32*PLUS
#2: Protein Terminase small subunit / DNA-packaging protein Nu1 / Gene product Nu1 / gpNu1


Mass: 11472.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: All alpha proteins, Putative DNA-binding domain, Hetero-dimer complex, Terminase gpNU1 subunit domain, Bacteriophage lambda The first three Ala residues at the beginning of the sequence from ...Details: All alpha proteins, Putative DNA-binding domain, Hetero-dimer complex, Terminase gpNU1 subunit domain, Bacteriophage lambda The first three Ala residues at the beginning of the sequence from coordinates come from the purification tag.
Source: (gene. exp.) Escherichia virus Lambda / Gene: Nu1, lambdap01
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P03707
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2M Ammonium Sulfate, 0.1M AcONa pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→50.5 Å / Num. obs: 5163 / % possible obs: 97.7 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 11.1 / Num. measured all: 18007 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.183.60.10530178320.9920.0660.1256.798.7
9-50.530.0446592180.9910.030.05415.595.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
autoPROCdata collection
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HLK, 1J9I

6hlk

1j9i


Resolution: 3→50.5 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.841 / SU B: 0.01 / SU ML: 0 / SU R Cruickshank DPI: 0.5774 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.577 / ESU R Free: 0.614
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3321 509 9.9 %RANDOM
Rwork0.3124 ---
obs0.3143 4654 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.1 Å2 / Biso mean: 67.198 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--9.57 Å20 Å20 Å2
2--20.02 Å20 Å2
3----10.46 Å2
Refinement stepCycle: final / Resolution: 3→50.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 0 20 1604
Biso mean---54.45 -
Num. residues----204
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 38 -
Rwork0.387 351 -
all-389 -
obs--98.73 %

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