[English] 日本語
Yorodumi
- PDB-3o0e: Crystal structure of OmpF in complex with colicin peptide OBS1 -

+
Open data


ID or keywords:

Loading...

-
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


colicin transmembrane transporter activity / extrachromosomal circular DNA / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding ...colicin transmembrane transporter activity / extrachromosomal circular DNA / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion channel activity / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / protein domain specific binding / lipid binding / protein-containing complex / identical protein binding / membrane / metal ion binding
Similarity search - Function
Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / 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-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / 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, Gram-negative type / Porin / His-Me finger superfamily / Porin domain superfamily / Porin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more