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- PDB-1tol: FUSION OF N-TERMINAL DOMAIN OF THE MINOR COAT PROTEIN FROM GENE I... -

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Basic information

Entry
Database: PDB / ID: 1tol
TitleFUSION OF N-TERMINAL DOMAIN OF THE MINOR COAT PROTEIN FROM GENE III IN PHAGE M13, AND C-TERMINAL DOMAIN OF E. COLI PROTEIN-TOLA
ComponentsPROTEIN (FUSION PROTEIN CONSISTING OF MINOR COAT PROTEIN, GLYCINE RICH LINKER, TOLA, AND A HIS TAG)
KeywordsVIRAL PROTEIN / BACTERIOPHAGE M13 / PHAGE INFECTION / TOL PATHWAY / FUSION PROTEIN
Function / homology
Function and homology information


cellular response to bacteriocin / cell septum assembly / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / cell division site / host cell membrane / disordered domain specific binding ...cellular response to bacteriocin / cell septum assembly / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / cell division site / host cell membrane / disordered domain specific binding / protein domain specific binding / cell division / symbiont entry into host cell / membrane / plasma membrane
Similarity search - Function
Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / 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 / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / TolA C-terminal / Tol-Pal system, TolA ...Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / 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 / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / TolA C-terminal / Tol-Pal system, TolA / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Attachment protein / Tol-Pal system protein TolA
Similarity search - Component
Biological speciesEnterobacteria phage M13 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.85 Å
AuthorsLubkowski, J. / Wlodawer, A. / Hennecke, F. / Plueckthun, A.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.
Authors: Lubkowski, J. / Hennecke, F. / Pluckthun, A. / Wlodawer, A.
History
DepositionMay 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FUSION PROTEIN CONSISTING OF MINOR COAT PROTEIN, GLYCINE RICH LINKER, TOLA, AND A HIS TAG)


Theoretical massNumber of molelcules
Total (without water)22,8511
Polymers22,8511
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.880, 88.880, 63.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (FUSION PROTEIN CONSISTING OF MINOR COAT PROTEIN, GLYCINE RICH LINKER, TOLA, AND A HIS TAG)


Mass: 22851.123 Da / Num. of mol.: 1
Fragment: N-TERMINAL DOMAIN OF MINOR COAT PROTEIN AND C-TERMINAL DOMAIN OF TOLA
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN COMPRISES RESIDUES 1-86 OF MATURE MINOR COAT PROTEIN FROM GENE III, INCLUDING GLYCINE-RICH LINKER (GGGSEGGGSEGGGSEGGG), AND RESIDUES 295-421 OF TOLA, AND C-TERMINAL TAIL WITH SEQUENCE AAAHHHHHH
Source: (gene. exp.) Enterobacteria phage M13 (virus), (gene. exp.) Escherichia coli (E. coli)
Genus: Inovirus, Escherichia / Species: , / Description: FUSION GENE / Plasmid: PTFT74 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0N8P2C2, UniProt: P19934
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Description: MIRAS WAS SUPPORTED BY MOLECULAR REPLACEMENT USING N-TERMINAL DOMAIN FROM PREVIOUSLY SOLVED STRUCTURE OF G3P (1G3P) AS A STARTING MODEL
Crystal growpH: 7.5
Details: PROTEIN AT CONCENTRATION 8-12 MG/ML IN 50 MM HEPES (PH=7.5) WITH ADDITION OF DTT C=2MM, WAS CRYSTALLIZED USING VAPOR DIFFUSION FROM THE SITTING OR HANGING DROP, WITH THE SOLUTION CONTAINING ...Details: PROTEIN AT CONCENTRATION 8-12 MG/ML IN 50 MM HEPES (PH=7.5) WITH ADDITION OF DTT C=2MM, WAS CRYSTALLIZED USING VAPOR DIFFUSION FROM THE SITTING OR HANGING DROP, WITH THE SOLUTION CONTAINING 25% PEG4000, 0.08M TRIS (PH=8.5), AND 0.15 M SODIUM ACETATE AS A PRECIPITANT. BEFORE SETTING THE DROPS, PROTEIN SOLUTION WAS MIXED WITH THE PRECIPITANT IN THE RATIO 1:1. CRYSTALS WERE GROWING BEST AT TEMPERATURE 15 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98
DetectorType: ADSC / Detector: CCD / Date: Apr 1, 1998 / Details: MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 22243 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 36.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 8.05 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 5.85 / % possible all: 100
Reflection
*PLUS
Num. measured all: 190164
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
PHASESphasing
SHARPphasing
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.85→10 Å / Num. parameters: 5335 / Num. restraintsaints: 4829 / Cross valid method: FREE-R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1534 7 %RANDOM
all0.2297 22065 --
obs0.2275 -99.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1325
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 159 1331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.085
X-RAY DIFFRACTIONs_approx_iso_adps0

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