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- PDB-2x9a: crystal structure of g3p from phage IF1 in complex with its corec... -

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Basic information

Entry
Database: PDB / ID: 2x9a
Titlecrystal structure of g3p from phage IF1 in complex with its coreceptor, the C-terminal domain of TolA
Components
  • ATTACHMENT PROTEIN G3P
  • MEMBRANE SPANNING PROTEIN, REQUIRED FOR OUTER MEMBRANE INTEGRITY
KeywordsVIRAL PROTEIN / TRANSMEMBRANE / PHAGE INFECTION / PHAGE RECOGNITION / HOST-VIRUS INTERACTION / VIRION / HOST MEMBRANE
Function / homology
Function and homology information


: / viral extrusion / virion attachment to host cell pilus / bacteriocin transport / toxin transmembrane transporter activity / adhesion receptor-mediated virion attachment to host cell / host cell membrane / viral capsid / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / membrane
Similarity search - Function
TolA C-terminal / Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / Tol-Pal system, TolA / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Roll ...TolA C-terminal / Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / Tol-Pal system, TolA / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Attachment protein G3P / Cell envelope integrity inner membrane protein TolA
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE IF1 (virus)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsLorenz, S.H. / Jakob, R.P. / 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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Dec 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

Downloads & links

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Assembly

Deposited unit
A: ATTACHMENT PROTEIN G3P
B: MEMBRANE SPANNING PROTEIN, REQUIRED FOR OUTER MEMBRANE INTEGRITY
C: ATTACHMENT PROTEIN G3P
D: MEMBRANE SPANNING PROTEIN, REQUIRED FOR OUTER MEMBRANE INTEGRITY


Theoretical massNumber of molelcules
Total (without water)42,0464
Polymers42,0464
Non-polymers00
Water1,04558
1
C: ATTACHMENT PROTEIN G3P
D: MEMBRANE SPANNING PROTEIN, REQUIRED FOR OUTER MEMBRANE INTEGRITY


Theoretical massNumber of molelcules
Total (without water)21,0232
Polymers21,0232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-6.4 kcal/mol
Surface area7520 Å2
MethodPISA
2
A: ATTACHMENT PROTEIN G3P
B: MEMBRANE SPANNING PROTEIN, REQUIRED FOR OUTER MEMBRANE INTEGRITY


Theoretical massNumber of molelcules
Total (without water)21,0232
Polymers21,0232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-6.2 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.515, 94.515, 132.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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: Protein MEMBRANE SPANNING PROTEIN, REQUIRED FOR OUTER MEMBRANE INTEGRITY / MEMBRANE SPANNING PROTEIN TOLA / TOLA


Mass: 13985.636 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 268-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8X965
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.7 Å3/Da / Density % sol: 54.46 % / Description: NONE
Crystal growpH: 4.5
Details: 0.1 M SODIUM CITRATE, 20 % PEG3350, 5 % MPD, PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: ID14-1 / Type: BESSY / Wavelength: 0.914
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 2.47→32.22 Å / Num. obs: 15411 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 4.25 % / Biso Wilson estimate: 55.89 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.02
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 4.15 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.17 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TOL

1tol


Resolution: 2.47→32.217 Å / SU ML: 0.34 / σ(F): 1.99 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 770 5 %
Rwork0.181 --
obs0.1834 15404 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.496 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1152 Å20 Å20 Å2
2---1.1152 Å20 Å2
3---2.2303 Å2
Refinement stepCycle: LAST / Resolution: 2.47→32.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 0 58 2338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072338
X-RAY DIFFRACTIONf_angle_d1.0323170
X-RAY DIFFRACTIONf_dihedral_angle_d19.7826
X-RAY DIFFRACTIONf_chiral_restr0.071340
X-RAY DIFFRACTIONf_plane_restr0.004416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4704-2.6610.30271500.24792849X-RAY DIFFRACTION95
2.661-2.92870.3221550.22662940X-RAY DIFFRACTION98
2.9287-3.35210.25571550.20392954X-RAY DIFFRACTION98
3.3521-4.22170.20151540.16132930X-RAY DIFFRACTION98
4.2217-32.220.19761560.15982961X-RAY DIFFRACTION99
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)
13.4482-0.8988-2.56713.193-0.02484.52450.0432-0.00640.21830.2712-0.38970.2696-0.0338-0.54150.31340.320.0380.00360.3629-0.15040.298523.5017-2.76821.523
23.7743-1.8326-0.59755.14762.17535.97590.0069-0.0404-0.27790.363-0.1269-0.27490.36440.23230.09560.30380.122-0.00020.26140.02310.332937.4665-15.1315-1.8124
33.3152-1.8798-0.75732.42081.06223.8393-0.33410.12390.0437-0.2782-0.0776-0.22220.54020.13720.34150.33650.02470.15730.35940.06430.346333.1369-8.294-23.4104
44.0385-0.8998-1.90473.28981.08395.0213-0.18060.0671-0.0436-0.0940.11260.3251-0.0014-0.41090.10720.18390.0162-0.02810.44570.01560.3815.4132-2.3528-20.0899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:62)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 332:421)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 2:62)
4X-RAY DIFFRACTION4(CHAIN D AND RESID 332:421)

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