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- PDB-9k2h: Crystal structure of the carboxy-terminal channel-forming domain ... -

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Basic information

Entry
Database: PDB / ID: 9k2h
TitleCrystal structure of the carboxy-terminal channel-forming domain of Colicin Ib
ComponentsColicin Ib protein
KeywordsANTIMICROBIAL PROTEIN / Pore-forming toxin / bacteriocin / colicin
Function / homology
Function and homology information


pore-forming activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 2b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsYang, J. / Hu, N.-J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)113-2311-B-055-004 Taiwan
CitationJournal: To Be Published
Title: The structure of colicin Ib channel-forming domain
Authors: Yang, J. / Hu, N.-J.
History
DepositionOct 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Colicin Ib protein


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)90.742, 90.742, 113.391
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 Ib protein


Mass: 23082.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2b (bacteria) / Gene: cib / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7DJZ6
Has protein modificationN

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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: 5.06 Å3/Da / Density meas: 0.652 Mg/m3 / Density % sol: 75.67 % / Description: Rod
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1% Nucleosides mix (2% w/v Cytidine, 2% w/v Inosine, 2% w/v Ribavirin, 2% w/v Thymidine, 2% w/v Uridine) 0.1M Buffer system 1(Imidazole; MES monohydrate (acid)) 30% precipitant mix(40% v/v ...Details: 1% Nucleosides mix (2% w/v Cytidine, 2% w/v Inosine, 2% w/v Ribavirin, 2% w/v Thymidine, 2% w/v Uridine) 0.1M Buffer system 1(Imidazole; MES monohydrate (acid)) 30% precipitant mix(40% v/v Glycerol; 20% w/v PEG 4000)
PH range: 5.2-6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→28.7 Å / Num. obs: 8332 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 35.2 Å2 / CC1/2: 0.857 / CC star: 0.961 / R split: 0.1 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.055 / Rrim(I) all: 0.116 / Rsym value: 0.065 / Χ2: 1.086 / Net I/av σ(I): 10.6 / Net I/σ(I): 16.3
Reflection shellResolution: 3.11→3.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8299 / CC1/2: 0.769 / CC star: 0.932 / R split: 0.03 / Rpim(I) all: 0.356 / Rrim(I) all: 0.712 / Rsym value: 0.426 / Χ2: 1.027 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→28.7 Å / SU ML: 0.2815 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.563
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 426 5.16 %
Rwork0.1984 7831 -
obs0.2002 8257 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 3.11→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 0 0 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091552
X-RAY DIFFRACTIONf_angle_d0.9092084
X-RAY DIFFRACTIONf_chiral_restr0.0465235
X-RAY DIFFRACTIONf_plane_restr0.008266
X-RAY DIFFRACTIONf_dihedral_angle_d22.8771577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.210.27731390.25162596X-RAY DIFFRACTION98.88
3.21-4.480.24651380.19852600X-RAY DIFFRACTION99.56
4.48-100.20931490.18162635X-RAY DIFFRACTION99.57
Refinement TLS params.Method: refined / Origin x: 14.5522613656 Å / Origin y: -13.8883289647 Å / Origin z: -18.941397464 Å
111213212223313233
T0.745168233175 Å2-0.00284099559399 Å20.0257908354795 Å2-0.353258082765 Å2-0.0434549870755 Å2--0.562371494959 Å2
L5.27823850884 °2-1.60112519822 °21.92070205416 °2-3.25308801167 °2-1.08334262603 °2--7.06369731949 °2
S-0.109227551673 Å °0.0280299386179 Å °0.257949334761 Å °-0.248051924028 Å °-0.077124501307 Å °0.132532106764 Å °-0.826230539242 Å °-0.190091673574 Å °0.250700744237 Å °
Refinement TLS groupSelection details: all

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