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- PDB-4eo1: crystal structure of the TolA binding domain from the filamentous... -

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Basic information

Entry
Database: PDB / ID: 4eo1
Titlecrystal structure of the TolA binding domain from the filamentous phage IKe
ComponentsAttachment protein G3P
KeywordsVIRAL PROTEIN / TolA binding protein / infection / G3P / filamentous phage / attachment protein / TolA binding / coat protein / TolA / phage coat / phage envelope of the 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
G3P, pilus binding domain / Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Roll / Mainly Beta
Similarity search - Domain/homology
Attachment protein G3P
Similarity search - Component
Biological speciesEnterobacteria phage Ike (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Attachment protein G3P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5122
Polymers7,4881
Non-polymers241
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.550, 33.810, 65.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: 7488.051 Da / Num. of mol.: 1 / Fragment: TolA binding domain, UNP residues 130-199
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 M (NH4)2SO4, 0.1 M Tris 8.5, 5% PEG400, 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: Jul 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→18.2 Å / Num. obs: 11481 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 15.93 Å2
Reflection shellResolution: 1.8→1.9 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2x9b

2x9b


Resolution: 1.8→18.16 Å / Cor.coef. Fo:Fc: 0.9267 / Cor.coef. Fo:Fc free: 0.9012 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 606 9.73 %RANDOM
Rwork0.1866 ---
all0.188 6232 --
obs0.1896 6230 --
Displacement parametersBiso mean: 19.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.5136 Å20 Å20 Å2
2--0.8397 Å20 Å2
3----2.3533 Å2
Refine analyzeLuzzati coordinate error obs: 0.196 Å
Refinement stepCycle: LAST / Resolution: 1.8→18.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms507 0 1 78 586
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.009509HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.34696HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d162SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes16HARMONIC2
X-RAY DIFFRACTIONt_gen_planes75HARMONIC5
X-RAY DIFFRACTIONt_it509HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.47
X-RAY DIFFRACTIONt_other_torsion15.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion65SEMIHARMONIC5
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_contact637SEMIHARMONIC4
LS refinement shellResolution: 1.8→2.01 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2229 160 9.26 %
Rwork0.1726 1567 -
all0.1771 1727 -
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)
10.6177-2.58520.55711.06760.06821.3195-0.0013-0.04060.09570.31950.1603-0.22980.05710.2136-0.1590.03010.0063-0.0484-0.0492-0.0297-0.04476.5305-6.520421.8655
20.7586-0.88720.62431.9515-0.6963.17360.0780.0093-0.1965-0.2110.00790.01940.1055-0.1128-0.086-0.04390.0054-0.0085-0.02390.006-0.0686-0.7886-11.14837.1183
30-0.4362-1.20793.4579-0.24465.47710.08410.0838-0.0477-0.1414-0.01410.1071-0.1837-0.1891-0.07-0.0480.0021-0.02410.0478-0.00650.0059-0.0766-12.20037.835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 10}A1 - 10
2X-RAY DIFFRACTION2{A|11 - 45}A11 - 45
3X-RAY DIFFRACTION3{A|46 - 66}A46 - 66

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