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- PDB-2ivz: Structure of TolB in complex with a peptide of the colicin E9 T- ... -

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Basic information

Entry
Database: PDB / ID: 2ivz
TitleStructure of TolB in complex with a peptide of the colicin E9 T- domain
Components
  • COLICIN-E9
  • PROTEIN TOLB
KeywordsPROTEIN TRANSPORT/HYDROLASE / PROTEIN-PROTEIN INTERACTION / PROTEIN TRANSPORT / BACTERIOCIN TRANSPORT / TOLB / COLICIN / PLASMID / NUCLEASE / HYDROLASE / TRANSPORT / ANTIBIOTIC / PERIPLASMIC / BACTERIOCIN / NATIVELY DISORDERED PROTEINS / PROTEIN TRANSPORT-HYDROLASE COMPLEX / ENDONUCLEASE / ANTIMICROBIAL / TRANSLOCATION
Function / homology
Function and homology information


cellular response to bacteriocin / regulation of membrane invagination / cell septum assembly / extrachromosomal circular DNA / bacteriocin transport / protein import / cell division site / protein transport / outer membrane-bounded periplasmic space / endonuclease activity ...cellular response to bacteriocin / regulation of membrane invagination / cell septum assembly / extrachromosomal circular DNA / bacteriocin transport / protein import / cell division site / protein transport / outer membrane-bounded periplasmic space / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / periplasmic space / defense response to bacterium / protein domain specific binding / cell division / protein-containing complex binding / protein-containing complex / metal ion binding / membrane
Similarity search - Function
TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / WD40-like beta propeller / WD40-like Beta Propeller Repeat / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 ...TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / WD40-like beta propeller / WD40-like Beta Propeller Repeat / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / TolB, C-terminal domain / His-Me finger superfamily / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Colicin-E9 / Tol-Pal system protein TolB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLoftus, S.R. / Walker, D. / Mate, M.J. / Bonsor, D.A. / James, R. / Moore, G.R. / Kleanthous, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Competitive Recruitment of the Periplasmic Translocation Portal Tolb by a Natively Disordered Domain of Colicin E9
Authors: Loftus, S.R. / Walker, D. / Mate, M.J. / Bonsor, D.A. / James, R. / Moore, G.R. / Kleanthous, C.
#1: Journal: Structure / Year: 1999
Title: Structure of the Escherichia Coli Tolb Protein Determined by MAD Methods at 1.95 A Resolution
Authors: Abergel, C. / Bouveret, E. / Claverie, J.-M. / Brown, K. / Rigal, A. / Lazdunski, C. / Benedetti, H.
#2: Journal: Structure / Year: 2000
Title: The Structure of Tolb, an Essential Component of the Tol-Dependent Translocation System, and its Protein-Protein Interaction with the Translocation Domain of Colicin E9.
Authors: Carr, S. / Penfold, C.N. / Bamford, V. / James, R. / Hemmings, A.M.
History
DepositionJun 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN TOLB
B: PROTEIN TOLB
C: PROTEIN TOLB
D: PROTEIN TOLB
E: COLICIN-E9
F: COLICIN-E9
G: COLICIN-E9
H: COLICIN-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,49715
Polymers195,2178
Non-polymers2817
Water22,3751242
1
A: PROTEIN TOLB
E: COLICIN-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8844
Polymers48,8042
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEIN TOLB
F: COLICIN-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8443
Polymers48,8042
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PROTEIN TOLB
G: COLICIN-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8844
Polymers48,8042
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PROTEIN TOLB
H: COLICIN-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8844
Polymers48,8042
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)130.092, 39.933, 154.848
Angle α, β, γ (deg.)90.00, 110.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN TOLB / TOLB


Mass: 47196.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A855
#2: Protein/peptide
COLICIN-E9 / COLICIN-E9 A CHAIN / RIBONUCLEASE


Mass: 1607.553 Da / Num. of mol.: 4 / Fragment: T-DOMAIN, RESIDUES 32-47 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
References: UniProt: P09883, Hydrolases; Acting on ester bonds
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1242 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPARTICIPATES IN THE UPTAKE OF GROUP A COLOCINS IN A TONB INDEPENDENT MANNER.THE PEPTIDE WHICH COMES ...PARTICIPATES IN THE UPTAKE OF GROUP A COLOCINS IN A TONB INDEPENDENT MANNER.THE PEPTIDE WHICH COMES FROM THE T-DOMAIN OF COLICIN IS INVOLVED IN INACTIVATION OF RIBOSOMES.

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5
Details: 24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→144 Å / Num. obs: 102162 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C5K

1c5k


Resolution: 2→144.34 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.705 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 5100 5 %RANDOM
Rwork0.168 ---
obs0.17 97047 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-1.06 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→144.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12269 0 7 1242 13518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9417235
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.36251630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41924.4575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3151872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3561577
X-RAY DIFFRACTIONr_chiral_restr0.1060.21844
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029965
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.25822
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.28678
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.21186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.2151
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9071.58306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47212968
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.26135062
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5054.54258
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 360
Rwork0.173 6990

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