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- PDB-8uut: Structure of Serratia entomophila antifeeding prophage Fibre foot... -

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Basic information

Entry
Database: PDB / ID: 8uut
TitleStructure of Serratia entomophila antifeeding prophage Fibre foot domain (Afp13)
ComponentsAnti-feeding prophage Fibre
KeywordsSTRUCTURAL PROTEIN / Anti-feeding prophage / Fibre foot / Cell binding
Function / homologyAttachment protein shaft domain superfamily / virion attachment to host cell / Afp13
Function and homology information
Biological speciesSerratia entomophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsYoung, P.G. / Hurst, M.R.H.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Ministry of Business, Innovation and Employment (New Zealand)C10X1805 New Zealand
CitationJournal: To Be Published
Title: Structure of Serratia entomophila antifeeding prophage Fibre foot domain (Afp13)
Authors: Young, P.G. / Hurst, M.R.H.
History
DepositionNov 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-feeding prophage Fibre
B: Anti-feeding prophage Fibre
C: Anti-feeding prophage Fibre
D: Anti-feeding prophage Fibre
E: Anti-feeding prophage Fibre
F: Anti-feeding prophage Fibre


Theoretical massNumber of molelcules
Total (without water)98,1086
Polymers98,1086
Non-polymers00
Water10,124562
1
A: Anti-feeding prophage Fibre
B: Anti-feeding prophage Fibre
C: Anti-feeding prophage Fibre


Theoretical massNumber of molelcules
Total (without water)49,0543
Polymers49,0543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-59 kcal/mol
Surface area13450 Å2
MethodPISA
2
D: Anti-feeding prophage Fibre
E: Anti-feeding prophage Fibre
F: Anti-feeding prophage Fibre


Theoretical massNumber of molelcules
Total (without water)49,0543
Polymers49,0543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-58 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.559, 130.559, 76.409
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11D-221-

HOH

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Components

#1: Protein
Anti-feeding prophage Fibre / Afp13


Mass: 16351.297 Da / Num. of mol.: 6 / Fragment: foot domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia entomophila (bacteria) / Strain: A1MO2 / Gene: afp13 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): SHuffle T7 / References: UniProt: Q6HAC6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.92 Å3/Da / Density % sol: 35.81 % / Description: Tear drop
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M Tri sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.83→45.45 Å / Num. obs: 64474 / % possible obs: 97.4 % / Redundancy: 43 % / Biso Wilson estimate: 20.51 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.073 / Net I/σ(I): 9.8
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 42.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3940 / CC1/2: 0.742 / Rpim(I) all: 0.622 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→45.45 Å / SU ML: 0.1992 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.891
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 3305 5.13 %
Rwork0.1805 61144 -
obs0.1824 64449 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 1.83→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5262 0 0 562 5824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00665380
X-RAY DIFFRACTIONf_angle_d0.92957303
X-RAY DIFFRACTIONf_chiral_restr0.0585829
X-RAY DIFFRACTIONf_plane_restr0.0053907
X-RAY DIFFRACTIONf_dihedral_angle_d6.8455776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.860.31991170.27432496X-RAY DIFFRACTION95.61
1.86-1.880.32161250.23852545X-RAY DIFFRACTION96.56
1.88-1.910.24781210.2342537X-RAY DIFFRACTION96.76
1.91-1.940.29121560.22292490X-RAY DIFFRACTION97.35
1.94-1.980.23531180.22152548X-RAY DIFFRACTION96.95
1.98-2.010.27521640.20912523X-RAY DIFFRACTION97.25
2.01-2.050.2371310.21122515X-RAY DIFFRACTION97.24
2.05-2.090.26431490.19732563X-RAY DIFFRACTION97.48
2.09-2.140.26271480.20982486X-RAY DIFFRACTION97.63
2.14-2.190.24961380.1972542X-RAY DIFFRACTION97.17
2.19-2.240.23511340.19552528X-RAY DIFFRACTION97.54
2.24-2.30.20631360.19182585X-RAY DIFFRACTION97.81
2.3-2.370.20111220.19622526X-RAY DIFFRACTION96.57
2.37-2.450.26571160.20462365X-RAY DIFFRACTION90.38
2.45-2.540.24131370.2112506X-RAY DIFFRACTION95.35
2.54-2.640.27651520.20262554X-RAY DIFFRACTION98.04
2.64-2.760.23941380.20012572X-RAY DIFFRACTION98.72
2.76-2.90.2531360.1932625X-RAY DIFFRACTION98.89
2.9-3.090.21641390.18842566X-RAY DIFFRACTION98.15
3.09-3.320.2091590.17652583X-RAY DIFFRACTION98.63
3.32-3.660.17921430.15072620X-RAY DIFFRACTION98.86
3.66-4.190.17711590.13192608X-RAY DIFFRACTION98.36
4.19-5.270.14781290.12532493X-RAY DIFFRACTION93.38
5.28-45.450.18231380.17382768X-RAY DIFFRACTION99.18

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