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Basic information

Entry
Database: PDB / ID: 8iom
TitleCrystal structure of the carboxy-terminal channel-forming domain of Colicin Ib
ComponentsColicin 1B
KeywordsANTIMICROBIAL PROTEIN / pore-forming toxin / antibacterial protein / colicin
Function / homology
Function and homology information


cytolysis / defense response to Gram-negative bacterium / membrane
Similarity search - Function
Channel forming colicin, N-terminal domain superfamily / Channel forming colicin, central receptor recognition / Colicin Ia / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature.
Similarity search - Domain/homology
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYang, J. / Hu, N.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)110-2311-B-005-005-MY3 Taiwan
CitationJournal: To Be Published
Title: Structure of colicin Ib Channel domain at 3.0 Angstroms resolution
Authors: Yang, J.
History
DepositionMar 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_seq_id / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num
Description: Sequence discrepancy
Details: renumber the residues and atoms to full-length colicin Ib residue numbers
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Colicin 1B


Theoretical massNumber of molelcules
Total (without water)23,0831
Polymers23,0831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.994, 91.994, 113.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Colicin 1B


Mass: 23082.576 Da / Num. of mol.: 1 / Fragment: channel-forming domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 3160_NCHU22 / Gene: CBL31_01480 / Plasmid: pQE70 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A200P0K8

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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: 5.26 Å3/Da / Density meas: 0.0003158 Mg/m3 / Density % sol: 76.61 % / Description: rectangular prism shape
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Precipitant: 0.1M sodium chloride, 0.1M sodium HEPES pH7.5, 12% w/v PEG 4000, 0.5 microliter 8mg/ml colicin Ib C domain mix with the same volume precipitant in the drop colicin Ib C domain ...Details: Precipitant: 0.1M sodium chloride, 0.1M sodium HEPES pH7.5, 12% w/v PEG 4000, 0.5 microliter 8mg/ml colicin Ib C domain mix with the same volume precipitant in the drop colicin Ib C domain buffer:20mM sodium, citrate pH5.2, 200mM NaCl
PH range: 5.2-7.5 / Temp details: 1/20 celsius

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→30 Å / Num. all: 11058 / Num. obs: 11040 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 54.03 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.047 / Rrim(I) all: 0.101 / Rsym value: 0.053 / Χ2: 0.868 / Net I/σ(I): 9
Reflection shellResolution: 2.94→3.06 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.556 / Num. unique obs: 1107 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.289 / Rrim(I) all: 0.627 / Rsym value: 0.399 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data collection
HKL-2000data scaling
PHENIX1.20.1_4487model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→26.08 Å / SU ML: 0.3408 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2189 904 9.88 %
Rwork0.1962 8247 -
obs0.1985 9151 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.3 Å2
Refinement stepCycle: LAST / Resolution: 3→26.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 0 0 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291552
X-RAY DIFFRACTIONf_angle_d0.54392084
X-RAY DIFFRACTIONf_chiral_restr0.0406235
X-RAY DIFFRACTIONf_plane_restr0.0032266
X-RAY DIFFRACTIONf_dihedral_angle_d13.3337205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.33161250.29521126X-RAY DIFFRACTION78.78
3.19-3.430.30261540.25911381X-RAY DIFFRACTION98.84
3.43-3.780.25631550.21521426X-RAY DIFFRACTION99.94
3.78-4.320.21211560.18461438X-RAY DIFFRACTION100
4.32-5.430.19191570.17091426X-RAY DIFFRACTION99.94
5.44-26.080.15721570.1591450X-RAY DIFFRACTION99.88
Refinement TLS params.Method: refined / Origin x: 14.1581513747 Å / Origin y: -14.7555243867 Å / Origin z: -8.56515684354 Å
111213212223313233
T0.233263507179 Å20.00873922485158 Å2-0.00757791923456 Å2-0.294008863687 Å20.0158329807647 Å2--0.28152442102 Å2
L1.04916145155 °2-0.347785486752 °2-0.396071211126 °2-0.868800950423 °20.404634742419 °2--2.3345264988 °2
S-0.00979578397846 Å °0.0195326023392 Å °0.0335585845808 Å °0.0632192913927 Å °-0.027696316799 Å °-0.047224786027 Å °-0.0668563173908 Å °-0.110548679571 Å °6.06189290359E-5 Å °
Refinement TLS groupSelection details: all

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