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- PDB-8on5: Structure of the tail fibre from an extracellular contractile inj... -

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Basic information

Entry
Database: PDB / ID: 8on5
TitleStructure of the tail fibre from an extracellular contractile injection system from Photorhabdus bacteria
ComponentsAdenoviral fiber protein
KeywordsCELL ADHESION / Tail fibre from an extracellular contractile injection system from bacteria / cell surface recognition / PVC / cell surface attachment / virulence.
Function / homologyAttachment protein shaft domain superfamily / virion attachment to host cell / Adenoviral fiber protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica subsp. asymbiotica ATCC 43949 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGodfrey, A.E. / Diaz-Saez, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MRC DTP in IBR United Kingdom
CitationJournal: To Be Published
Title: Structure of the tail fibre from an extracellular contractile injection system from Photorhabdus bacteria
Authors: Godfrey, A.E. / Diaz-Saez, L.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenoviral fiber protein
B: Adenoviral fiber protein
C: Adenoviral fiber protein
D: Adenoviral fiber protein
E: Adenoviral fiber protein
F: Adenoviral fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,36427
Polymers141,5676
Non-polymers1,79621
Water9,314517
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Both the structure and gel filtration confirm the hexamer formation as the biological assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60130 Å2
ΔGint-480 kcal/mol
Surface area46410 Å2
Unit cell
Length a, b, c (Å)67.458, 53.536, 220.660
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Adenoviral fiber protein


Mass: 23594.537 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949 (bacteria)
Gene: PAU_02236 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7BKQ5
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 56.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.02 M CaCl2 dihydrate, 0.1M Na acetate pH 4.6, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.3→60.03 Å / Num. obs: 70537 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 37.715 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.046 / Rrim(I) all: 0.113 / Χ2: 0.96 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.35 Å / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.669 / Num. measured all: 26868 / Num. unique obs: 4480 / CC1/2: 0.941 / Rpim(I) all: 0.301 / Rrim(I) all: 0.735 / Χ2: 1.01 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→60.03 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.376 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23582 3581 5.1 %RANDOM
Rwork0.17902 ---
obs0.18191 66849 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.635 Å2
Baniso -1Baniso -2Baniso -3
1--3.71 Å20 Å2-3.47 Å2
2--2.05 Å2-0 Å2
3---2.3 Å2
Refinement stepCycle: 1 / Resolution: 2.3→60.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9109 0 122 517 9748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129573
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169260
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.64613031
X-RAY DIFFRACTIONr_angle_other_deg0.4851.57221384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.90851273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.362547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.831101612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.21459
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022071
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_it4.1454.344879
X-RAY DIFFRACTIONr_mcbond_other4.1444.3394879
X-RAY DIFFRACTIONr_mcangle_it5.9717.7896110
X-RAY DIFFRACTIONr_mcangle_other5.977.7896111
X-RAY DIFFRACTIONr_scbond_it4.5084.7084694
X-RAY DIFFRACTIONr_scbond_other4.5074.7084695
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8588.4756882
X-RAY DIFFRACTIONr_long_range_B_refined8.75853.0210506
X-RAY DIFFRACTIONr_long_range_B_other8.75753.0210507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 267 -
Rwork0.284 4878 -
obs--99.83 %

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