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- PDB-8uur: Structure of Serratia proteamaculans antifeeding prophage mini-fi... -

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Basic information

Entry
Database: PDB / ID: 8uur
TitleStructure of Serratia proteamaculans antifeeding prophage mini-fibre (AfpX13)
ComponentsAfpX13
KeywordsSTRUCTURAL PROTEIN / Anti-feeding prophage / Fibre foot / Cell binding
Function / homologyAttachment protein shaft domain superfamily / Parallel beta-helix repeat / Parallel beta-helix repeats / virion attachment to host cell / : / AfpX13
Function and homology information
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.0Aug 27, 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: AfpX13
B: AfpX13
C: AfpX13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7726
Polymers86,4343
Non-polymers3373
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20360 Å2
ΔGint-159 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.556, 68.409, 132.757
Angle α, β, γ (deg.)90.000, 93.323, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein AfpX13


Mass: 28811.461 Da / Num. of mol.: 3 / Mutation: residues 125-438 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (bacteria) / Strain: AGR96X / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): ShuffleT7 / References: UniProt: A0A2R2Q2I2
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.59 Å3/Da / Density % sol: 65.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 8% PEG 3350, 0.1 M HEPES pH 7.5, 20 mM CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953725 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 2.5→45.47 Å / Num. obs: 36902 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 34.27 Å2 / CC1/2: 0.984 / Rpim(I) all: 0.124 / Net I/σ(I): 5.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4143 / CC1/2: 0.482 / Rpim(I) all: 0.668 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.47 Å / SU ML: 0.343 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1531
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2636 1858 5.04 %
Rwork0.2173 35002 -
obs0.2197 36860 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5160 0 3 220 5383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815238
X-RAY DIFFRACTIONf_angle_d1.03517101
X-RAY DIFFRACTIONf_chiral_restr0.0605837
X-RAY DIFFRACTIONf_plane_restr0.0054912
X-RAY DIFFRACTIONf_dihedral_angle_d6.8198753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.33661320.2912685X-RAY DIFFRACTION99.75
2.57-2.640.34221440.27842682X-RAY DIFFRACTION99.75
2.64-2.730.34551530.26442673X-RAY DIFFRACTION99.79
2.73-2.830.28341590.24962688X-RAY DIFFRACTION99.82
2.83-2.940.26571240.23352654X-RAY DIFFRACTION99.93
2.94-3.070.29461210.2242710X-RAY DIFFRACTION99.65
3.07-3.230.29331190.21252746X-RAY DIFFRACTION99.76
3.23-3.440.23581330.21332674X-RAY DIFFRACTION99.68
3.44-3.70.26631820.20552638X-RAY DIFFRACTION99.54
3.7-4.080.24261500.21292696X-RAY DIFFRACTION99.68
4.08-4.660.24091500.18772675X-RAY DIFFRACTION98.98
4.66-5.870.23021390.20322720X-RAY DIFFRACTION99.24
5.88-45.470.25441520.21022761X-RAY DIFFRACTION98.71

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