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- PDB-3o0e: Crystal structure of OmpF in complex with colicin peptide OBS1 -

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Basic information

Entry
Database: PDB / ID: 3o0e
TitleCrystal structure of OmpF in complex with colicin peptide OBS1
Components
  • Colicin-E9
  • Porin OmpF
KeywordsMEMBRANE PROTEIN / porin / complex / colicin
Function / homology
Function and homology information


extrachromosomal circular DNA / colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding ...extrachromosomal circular DNA / colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / endonuclease activity / monoatomic ion transmembrane transport / Hydrolases; Acting on ester bonds / protein domain specific binding / lipid binding / protein-containing complex / membrane / identical protein binding
Similarity search - Function
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 / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site ...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 / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin / Porin, Gram-negative type / : / Porin domain superfamily / Porin / His-Me finger superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Porin OmpF / Outer membrane porin F / Colicin-E9
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsWojdyla, J.A. / Housden, N.G. / Korczynska, J. / Grishkovskaya, I. / Kirkpatrick, N. / Brzozowski, A.M. / Kleanthous, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF.
Authors: Housden, N.G. / Wojdyla, J.A. / Korczynska, J. / Grishkovskaya, I. / Kirkpatrick, N. / Brzozowski, A.M. / Kleanthous, C.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0May 5, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / cell / chem_comp / diffrn / entity / entity_src_nat / exptl_crystal_grow / pdbx_audit_support / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _chem_comp.pdbx_synonyms ..._cell.volume / _chem_comp.pdbx_synonyms / _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _exptl_crystal_grow.method / _pdbx_database_status.SG_entry / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_all / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.occupancy_max / _refine.occupancy_min / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns.number_all / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct.pdbx_CASP_flag / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_ncs_ens.id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id / _symmetry.space_group_name_Hall
Description: Model orientation/position
Details: The direction of OBS1 peptide was re-built, following new experimental data that shows the directionality in which the peptide binds within the OmpF pore.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_ls_shell
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_ls_shell.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Porin OmpF
B: Porin OmpF
C: Porin OmpF
D: Porin OmpF
E: Porin OmpF
F: Porin OmpF
L: Colicin-E9
M: Colicin-E9
N: Colicin-E9
O: Colicin-E9
P: Colicin-E9
Q: Colicin-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,78518
Polymers232,03112
Non-polymers1,7546
Water75742
1
A: Porin OmpF
C: Porin OmpF
E: Porin OmpF
L: Colicin-E9
N: Colicin-E9
P: Colicin-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8929
Polymers116,0156
Non-polymers8773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Porin OmpF
D: Porin OmpF
F: Porin OmpF
M: Colicin-E9
O: Colicin-E9
Q: Colicin-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8929
Polymers116,0156
Non-polymers8773
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.491, 101.618, 162.142
Angle α, β, γ (deg.)90.000, 94.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_1ens_2(chain "L" and resid 2 through 14)
d_2ens_2chain "M"
d_3ens_2chain "N"
d_4ens_2(chain "O" and resid 2 through 14)
d_5ens_2chain "P"
d_6ens_2(chain "Q" and resid 2 through 14)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAPHEA1 - 340
d_12ens_1BOGBOGB
d_21ens_1ALAPHEC1 - 340
d_22ens_1BOGBOGD
d_31ens_1ALAPHEE1 - 340
d_32ens_1BOGBOGF
d_41ens_1ALAPHEG1 - 340
d_42ens_1BOGBOGH
d_51ens_1ALAPHEI1 - 340
d_52ens_1BOGBOGJ
d_61ens_1ALAPHEK1 - 340
d_62ens_1BOGBOGL
d_11ens_2SERHISM1 - 13
d_21ens_2SERHISN1 - 13
d_31ens_2SERHISO1 - 13
d_41ens_2SERHISP1 - 13
d_51ens_2SERHISQ1 - 13
d_61ens_2SERHISR1 - 13

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein
Porin OmpF


Mass: 37114.250 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BE3000 / References: UniProt: A0A418U3R0, UniProt: P02931*PLUS
#2: Protein/peptide
Colicin-E9


Mass: 1557.523 Da / Num. of mol.: 6 / Fragment: UNP Residues 2-18 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Escherichia coli (E. coli)
References: UniProt: P09883, Hydrolases; Acting on ester bonds
#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.2M Li2SO4, 0.1M sodium cacodylate, pH 6.5, sitting drop vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9689 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9689 Å / Relative weight: 1
ReflectionResolution: 3→20.12 Å / Num. obs: 47846 / % possible obs: 72.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 87.45 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.232 / Num. unique obs: 65923 / % possible all: 17.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OPF

1opf


Resolution: 3.01→20 Å / SU ML: 0.4608 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 37.4756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3025 2393 5.04 %RANDOM
Rwork0.2651 45089 --
obs0.2669 47482 73.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.31 Å2
Refinement stepCycle: LAST / Resolution: 3.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16304 0 120 42 16466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216766
X-RAY DIFFRACTIONf_angle_d0.518822652
X-RAY DIFFRACTIONf_chiral_restr0.04332299
X-RAY DIFFRACTIONf_plane_restr0.00213047
X-RAY DIFFRACTIONf_dihedral_angle_d6.07262405
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.551461702759
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.513280466406
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.69942504779
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.575409266954
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.523976899294
ens_2d_2MX-RAY DIFFRACTIONTorsion NCS1.98341853386
ens_2d_3MX-RAY DIFFRACTIONTorsion NCS1.93654528727
ens_2d_4MX-RAY DIFFRACTIONTorsion NCS1.41291642429
ens_2d_5MX-RAY DIFFRACTIONTorsion NCS2.11676653054
ens_2d_6MX-RAY DIFFRACTIONTorsion NCS1.79793428353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.080.3995250.4368598X-RAY DIFFRACTION16.28
3.08-3.140.3804340.3473784X-RAY DIFFRACTION21.67
3.14-3.210.4267510.3662990X-RAY DIFFRACTION27.58
3.22-3.290.3783670.34781260X-RAY DIFFRACTION34.61
3.3-3.380.3761880.33351591X-RAY DIFFRACTION44.25
3.38-3.480.3879910.33462125X-RAY DIFFRACTION58.69
3.48-3.590.36511550.32542711X-RAY DIFFRACTION75.36
3.59-3.720.33951970.32933180X-RAY DIFFRACTION89.22
3.72-3.870.32691850.30523482X-RAY DIFFRACTION95.67
3.87-4.040.31231690.28833548X-RAY DIFFRACTION97.69
4.04-4.260.36342040.27033542X-RAY DIFFRACTION98.24
4.26-4.520.24171670.24213569X-RAY DIFFRACTION98.26
4.52-4.860.26062000.24093553X-RAY DIFFRACTION97.91
4.86-5.350.28672050.22923559X-RAY DIFFRACTION97.79
5.35-6.10.25842010.22683517X-RAY DIFFRACTION97.51
6.1-7.620.26971720.24973592X-RAY DIFFRACTION97.19
7.62-200.32111820.25573488X-RAY DIFFRACTION93.24

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