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- PDB-1rh1: crystal structure of the cytotoxic bacterial protein colicin B at... -

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Basic information

Entry
Database: PDB / ID: 1rh1
Titlecrystal structure of the cytotoxic bacterial protein colicin B at 2.5 A resolution
ComponentsColicin B
KeywordsANTIBIOTIC / colicin B / FepA / cytotoxic bacterial protein / TonB
Function / homology
Function and homology information


cytolysis / : / defense response to Gram-negative bacterium / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Colicin / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / TonB-dependent receptor (TBDR) proteins signature 1. / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / Globin-like ...Colicin / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / TonB-dependent receptor (TBDR) proteins signature 1. / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / Globin-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHilsenbeck, J.L. / Park, H. / Chen, G. / Youn, B. / Postle, K. / Kang, C.
CitationJournal: Mol.Microbiol. / Year: 2004
Title: Crystal structure of the cytotoxic bacterial protein colicin B at 2.5 A resolution
Authors: Hilsenbeck, J.L. / Park, H. / Chen, G. / Youn, B. / Postle, K. / Kang, C.
History
DepositionNov 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Colicin B


Theoretical massNumber of molelcules
Total (without water)54,9111
Polymers54,9111
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.162, 138.167, 106.160
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Colicin B


Mass: 54910.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CBA / Plasmid: pES3 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P05819
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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: 4.41 Å3/Da / Density % sol: 72.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, PEG, Zn Acetate, octyl glucoside, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12-32 mg/mlprotein1drop
240 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
4100 mMMES1reservoirpH6.0
510 %PEG40001reservoir
6200 mM1reservoirZn(OAc)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9796,0.9183
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2002
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.91831
ReflectionResolution: 2.5→10 Å / Num. obs: 17631 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.0623 / Rsym value: 0.059 / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→10 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.246 8450 random 5%
Rwork0.197 --
all0.231 17631 -
obs0.224 16989 -
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3718 0 0 184 3902
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.414
X-RAY DIFFRACTIONx_bond_d0.0015
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.015

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