[English] 日本語
Yorodumi
- PDB-8iom: Crystal structure of the carboxy-terminal channel-forming domain ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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