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- PDB-5lye: Re-refined structure of the bacteriophage T4 short tail fibre PDB... -

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Basic information

Entry
Database: PDB / ID: 5lye
TitleRe-refined structure of the bacteriophage T4 short tail fibre PDB entry 1H6W containing 71 additionally identified residues
ComponentsGp12
KeywordsSTRUCTURAL PROTEIN / GENE PRODUCT 12 / ADHESIN / FIBROUS PROTEIN
Function / homology
Function and homology information


virus tail, fiber / metal ion binding
Similarity search - Function
Bacteriophage T4, Gp12 / Short tail fibre protein, C-terminal / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Short tail fibre protein receptor-binding domain / Phage tail collar domain / Phage tail collar domain superfamily / Phage Tail Collar Domain
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
Authorsvan Raaij, M.J. / Taylor, N.M.I. / Leiman, P.G.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBFU2014-53425-P Spain
Citation
Journal: Mol. Microbiol. / Year: 2018
Title: Contractile injection systems of bacteriophages and related systems.
Authors: Taylor, N.M.I. / van Raaij, M.J. / Leiman, P.G.
#1: Journal: Nature / Year: 2016
Title: Structure of the T4 baseplate and its function in triggering sheath contraction.
Authors: Nicholas M I Taylor / Nikolai S Prokhorov / Ricardo C Guerrero-Ferreira / Mikhail M Shneider / Christopher Browning / Kenneth N Goldie / Henning Stahlberg / Petr G Leiman /
Abstract: Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This ...Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.
#2: Journal: J. Mol. Biol. / Year: 2001
Title: Crystal structure of a heat and protease-stable part of the bacteriophage T4 short tail fibre.
Authors: van Raaij, M.J. / Schoehn, G. / Burda, M.R. / Miller, S.
#3: Journal: Biol. Chem. / Year: 2001
Title: Identification and crystallisation of a heat- and protease-stable fragment of the bacteriophage T4 short tail fibre.
Authors: van Raaij, M.J. / Schoehn, G. / Jaquinod, M. / Ashman, K. / Burda, M.R. / Miller, S.
History
DepositionSep 27, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionJan 17, 2018ID: 1H6W
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_special_symmetry
Item: _pdbx_database_related.content_type
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8354
Polymers33,6681
Non-polymers1673
Water4,071226
1
A: Gp12
hetero molecules

A: Gp12
hetero molecules

A: Gp12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,50612
Polymers101,0053
Non-polymers5019
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area28340 Å2
ΔGint-188 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.257, 51.257, 249.491
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-601-

CL

21A-865-

HOH

31A-874-

HOH

41A-899-

HOH

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Components

#1: Protein Gp12


Mass: 33668.434 Da / Num. of mol.: 1 / Fragment: Heat and Protease-stable fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T2 (virus) / Gene: 12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): JM109 / References: UniProt: Q38160*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE SHORT TAIL FIBRE OF BACTERIOPHAGE T4D HAS NOT BEEN DEPOSITED

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: Bars with hexagonal cross-section
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15-25 % (V/V) 2-METHYLPROPANE-2-OL (TERTIARY BUTANOL), 100 MM SODIUM CITRATE PH 5.6 10% (V/V) GLYCEROL, 10 MM HEPES, 150 MM SODIUM CHLORIDE
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→19.8 Å / Num. obs: 28682 / % possible obs: 92.3 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.12 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 4.8 / % possible all: 68.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5.8.0155refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→19.8 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 2.129 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21465 1452 5.1 %RANDOM
Rwork0.18317 ---
obs0.18473 27229 91.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 7 226 1967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191762
X-RAY DIFFRACTIONr_bond_other_d0.0020.021642
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9392393
X-RAY DIFFRACTIONr_angle_other_deg133764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.915233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53724.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03315277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0321511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022048
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02399
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7853.758941
X-RAY DIFFRACTIONr_mcbond_other2.7853.76940
X-RAY DIFFRACTIONr_mcangle_it4.2115.6141171
X-RAY DIFFRACTIONr_mcangle_other4.215.6131172
X-RAY DIFFRACTIONr_scbond_it2.7014.015820
X-RAY DIFFRACTIONr_scbond_other2.694.018813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3165.9421215
X-RAY DIFFRACTIONr_long_range_B_refined6.86344.8141956
X-RAY DIFFRACTIONr_long_range_B_other6.57844.6071903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 79 -
Rwork0.186 1348 -
obs--64.37 %

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