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- PDB-2x9b: The filamentous phages fd and IF1 use different infection mechanisms -

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Basic information

Entry
Database: PDB / ID: 2x9b
TitleThe filamentous phages fd and IF1 use different infection mechanisms
ComponentsATTACHMENT PROTEIN G3P
KeywordsVIRAL PROTEIN / VIRION / PHAGE RECOGNITION / HOST PHAGE COAT PROTEIN HOST-VIRUS INTERACTION
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
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 IF1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsLorenz, S.H. / Jakob, R.P. / Weininger, U. / Dobbek, H. / Schmid, F.X.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Filamentous Phages Fd and If1 Use Different Mechanisms to Infect Escherichia Coli.
Authors: Lorenz, S.H. / Jakob, R.P. / Weininger, U. / Balbach, J. / Dobbek, H. / Schmid, F.X.
History
DepositionMar 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATTACHMENT PROTEIN G3P
B: ATTACHMENT PROTEIN G3P


Theoretical massNumber of molelcules
Total (without water)14,0752
Polymers14,0752
Non-polymers00
Water86548
1
A: ATTACHMENT PROTEIN G3P


Theoretical massNumber of molelcules
Total (without water)7,0371
Polymers7,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATTACHMENT PROTEIN G3P


Theoretical massNumber of molelcules
Total (without water)7,0371
Polymers7,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.836, 106.836, 75.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein ATTACHMENT PROTEIN G3P / GENE 3 PROTEIN / MINOR COAT PROTEIN / G3P / IF1-N1


Mass: 7037.493 Da / Num. of mol.: 2 / Fragment: TOLA-BINDING DOMAIN, RESIDUES 17-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE IF1 (virus) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O80297
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 4.42 Å3/Da / Density % sol: 71.97 % / Description: NONE
Crystal growpH: 6.5
Details: 3 M NACL, 5 % MPD, 0.1 M CACL2, 0.1 M IMIDAZOL PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.914
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 2.92→31.72 Å / Num. obs: 5889 / % possible obs: 99.7 % / Observed criterion σ(I): 3.5 / Redundancy: 11.38 % / Biso Wilson estimate: 71.67 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.6
Reflection shellResolution: 2.92→3.26 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.87 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G3P

1g3p


Resolution: 2.92→31.72 Å / Cor.coef. Fo:Fc: 0.8726 / Cor.coef. Fo:Fc free: 0.8215 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 566 9.6 %RANDOM
Rwork0.2426 ---
obs0.245 5876 99.7 %-
Displacement parametersBiso mean: 54.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.0529 Å20 Å20 Å2
2--1.0529 Å20 Å2
3----2.1058 Å2
Refine analyzeLuzzati coordinate error obs: 0.452 Å
Refinement stepCycle: LAST / Resolution: 2.92→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 0 48 1002
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.007982HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.871341HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d311SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes143HARMONIC5
X-RAY DIFFRACTIONt_it982HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.68
X-RAY DIFFRACTIONt_other_torsion17.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion127SEMIHARMONIC5
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_contact1001SEMIHARMONIC4
LS refinement shellResolution: 2.92→3.26 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2537 153 9.44 %
Rwork0.2459 1467 -
all0.2466 1620 -
obs--100 %
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)
11.75051.08440.28612.5337-0.27043.4532-0.00690.08240.1332-0.0541-0.0572-0.0198-0.23210.09720.0641-0.0166-0.17840.0652-0.0127-0.01880.043238.6347-26.87869.2219
22.17922.1815-0.36574.92041.77872.7516-0.02220.3934-0.121-0.2760.05380.0410.0112-0.2477-0.03150.1879-0.0226-0.0793-0.0478-0.00530.022842.5017-3.032717.6625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A1 - A62 )
2X-RAY DIFFRACTION2(B1 - B61 )

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