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- PDB-4uw7: Structure of the carboxy-terminal domain of the bacteriophage T5 ... -

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Basic information

Entry
Database: PDB / ID: 4uw7
TitleStructure of the carboxy-terminal domain of the bacteriophage T5 L- shaped tail fiber without its intra-molecular chaperone domain
ComponentsL-SHAPED TAIL FIBER PROTEIN
KeywordsVIRAL PROTEIN / BACTERIAL VIRUSES / CAUDOVIRALES / SIPHOVIRIDAE / INFECTION.
Function / homology
Function and homology information


lipopolysaccharide-mediated virion attachment to host cell / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / symbiont entry into host cell / proteolysis
Similarity search - Function
Intramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Side tail fiber protein pb1 / Side tail fiber protein pb1
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsGarcia-Doval, C. / Luque, D. / Caston, J.R. / Otero, J.M. / Llamas-Saiz, A.L. / Boulanger, P. / van Raaij, M.J.
Citation
Journal: Viruses / Year: 2015
Title: Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone.
Authors: Garcia-Doval, C. / Caston, J.R. / Luque, D. / Granell, M. / Otero, J.M. / Llamas-Saiz, A.L. / Renouard, M. / Boulanger, P. / van Raaij, M.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization of the C-Terminal Domain of the Bacteriophage T5 L-Shaped Fibre.
Authors: Garcia-Doval, C. / Luque, D. / Caston, J.R. / Boulanger, P. / van Raaij, M.J.
History
DepositionAug 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references / Structure summary
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
A: L-SHAPED TAIL FIBER PROTEIN
B: L-SHAPED TAIL FIBER PROTEIN
C: L-SHAPED TAIL FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5126
Polymers93,2363
Non-polymers2763
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39640 Å2
ΔGint-284.5 kcal/mol
Surface area30770 Å2
MethodPQS
Unit cell
Length a, b, c (Å)227.430, 58.180, 69.910
Angle α, β, γ (deg.)90.00, 98.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-991-

PHE

21B-2003-

HOH

31C-2001-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA990 - 126221 - 293
21SERSERBB990 - 126221 - 293
12SERSERAA990 - 126221 - 293
22SERSERCC990 - 126221 - 293
13CYSCYSBB989 - 126220 - 293
23CYSCYSCC989 - 126220 - 293

NCS ensembles :
ID
1
2
3

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Components

#1: Protein L-SHAPED TAIL FIBER PROTEIN / L-SHAPED TAIL FIBRES


Mass: 31078.691 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN, RESIDUES 970-1263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T5 (virus) / Plasmid: PET-28A / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 DE3 / References: UniProt: Q5DMH0, UniProt: P13390*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS-HCL PH 8.5, 17.5% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9797
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013 / Details: HORIZONTAL AND VERTICAL FOCUSSING MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.52→56.2 Å / Num. obs: 30585 / % possible obs: 96.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.52→56.19 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.622 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26607 2035 6.7 %THIN SHELLS
Rwork0.21339 ---
obs0.21704 28484 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å21.05 Å2
2--3.67 Å20 Å2
3----4.41 Å2
Refinement stepCycle: LAST / Resolution: 2.52→56.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 18 109 6247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196312
X-RAY DIFFRACTIONr_bond_other_d0.0050.025816
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9468590
X-RAY DIFFRACTIONr_angle_other_deg0.971313355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217378
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021512
X-RAY DIFFRACTIONr_nbd_refined0.2020.21245
X-RAY DIFFRACTIONr_nbd_other0.1910.26284
X-RAY DIFFRACTIONr_nbtor_refined0.180.23100
X-RAY DIFFRACTIONr_nbtor_other0.0870.23520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0250.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8584.8823303
X-RAY DIFFRACTIONr_mcbond_other3.8594.8823302
X-RAY DIFFRACTIONr_mcangle_it5.6657.3194125
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9295.2513009
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0457.7274462
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A13484
12B13484
21A13486
22C13486
31B13537
32C13537
LS refinement shellResolution: 2.52→2.656 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.377 201 -
Rwork0.325 4242 -
obs--99.06 %

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