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- PDB-4eo0: crystal structure of the pilus binding domain of the filamentous ... -

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Basic information

Entry
Database: PDB / ID: 4eo0
Titlecrystal structure of the pilus binding domain of the filamentous phage IKe
ComponentsAttachment protein G3P
KeywordsVIRAL PROTEIN / filamentuos phage / infection / pilus binding / gene-3-protein / g3p / receptor binding / N-Pilus / at the tip of filamentous phage IKe
Function / homology
Function and homology information


viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / host cell membrane / viral capsid / entry receptor-mediated virion attachment to host cell / membrane
Similarity search - Function
Translation Initiation Factor IF3 - #160 / G3P, pilus binding domain / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Attachment protein G3P
Similarity search - Component
Biological speciesEnterobacteria phage Ike (virus)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.61 Å
AuthorsJakob, R.P. / Geitner, A.J. / Weininger, U. / Balbach, J. / Dobbek, H. / Schmid, F.X.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Structural and energetic basis of infection by the filamentous bacteriophage IKe.
Authors: Jakob, R.P. / Geitner, A.J. / Weininger, U. / Balbach, J. / Dobbek, H. / Schmid, F.X.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Attachment protein G3P


Theoretical massNumber of molelcules
Total (without water)12,8941
Polymers12,8941
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.300, 59.300, 137.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsAuthor states that the protein is a Monomer with all methods tested including Gel Filtration, DLS, DSC, protein folding/Stability experiments

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Components

#1: Protein Attachment protein G3P / Gene 3 protein / G3P / Minor coat protein


Mass: 12894.206 Da / Num. of mol.: 1 / Fragment: IKe pilus binding domain, UNP residues 20-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Ike (virus) / Gene: III / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P03663
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-20% PPG400 0.1 M Bis-Tris 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→24.94 Å / Num. obs: 16254 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.38 Å2 / Rmerge(I) obs: 0.09
Reflection shellResolution: 1.61→1.72 Å / Rmerge(I) obs: 0.28 / % possible all: 78.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.61→24.94 Å / Cor.coef. Fo:Fc: 0.9427 / Cor.coef. Fo:Fc free: 0.9425 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 1013 6.23 %RANDOM
Rwork0.1872 ---
all0.187 16256 --
obs0.1884 16254 --
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.2441 Å20 Å20 Å2
2---1.2441 Å20 Å2
3---2.4882 Å2
Refinement stepCycle: LAST / Resolution: 1.61→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 0 165 987
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.009890HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.041222HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d317SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes25HARMONIC2
X-RAY DIFFRACTIONt_gen_planes136HARMONIC5
X-RAY DIFFRACTIONt_it890HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion15.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion124SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1157SEMIHARMONIC4
LS refinement shellResolution: 1.61→1.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2892 174 6.06 %
Rwork0.254 2695 -
all0.2562 2869 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.78820.0286-0.48074.3546-0.04851.67630.1354-0.0246-0.1737-0.0255-0.2610.1329-0.088-0.09690.12560.02890.02720.0023-0.1015-0.01270.003855.00887.419513.9525
20.5758-0.1609-2.46010.65840.23281.3218-0.0488-0.00920.00650.046-0.0336-0.00730.07920.10840.08240.24390.07890.1443-0.01080.1520.201874.644435.3082-6.0953
30.1109-0.3491-0.33445.0683-0.53950.83950.11910.0722-0.026-0.5442-0.19180.35710.0465-0.04460.07260.09230.0563-0.0501-0.0677-0.00890.001554.40245.59117.1402
41.42150.3418-0.75716.7109-0.89551.27460.10210.08770.1286-0.2766-0.17170.1767-0.09010.01780.06960.04380.0326-0.0139-0.09540.0079-0.053156.567413.508711.0112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|4 - 18}A4 - 18
2X-RAY DIFFRACTION2{A|19 - 34}A19 - 34
3X-RAY DIFFRACTION3{A|35 - 72}A35 - 72
4X-RAY DIFFRACTION4{A|73 - 109}A73 - 109

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