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- PDB-3qdr: Structural characterization of the interaction of colicin A, coli... -

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Basic information

Entry
Database: PDB / ID: 3qdr
TitleStructural characterization of the interaction of colicin A, colicin N, and TolB with the TolAIII translocon
Components
  • Colicin-A
  • Protein tolA
KeywordsPROTEIN TRANSPORT/TOXIN / ColA / TolA / Complex / translocation / ColA binds to TolA / Methylation / PROTEIN TRANSPORT-TOXIN complex
Function / homology
Function and homology information


cellular response to bacteriocin / cell septum assembly / regulation of membrane invagination / bacteriocin transport / pore-forming activity / toxin transmembrane transporter activity / protein import / virion binding / cell division site / disordered domain specific binding ...cellular response to bacteriocin / cell septum assembly / regulation of membrane invagination / bacteriocin transport / pore-forming activity / toxin transmembrane transporter activity / protein import / virion binding / cell division site / disordered domain specific binding / defense response to Gram-negative bacterium / molecular adaptor activity / killing of cells of another organism / protein domain specific binding / symbiont entry into host cell / cell division / membrane / plasma membrane
Similarity search - Function
SH3 type barrels. - #970 / : / Colicin-A N-terminal domain / TolA C-terminal / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / Tol-Pal system, TolA / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain ...SH3 type barrels. - #970 / : / Colicin-A N-terminal domain / TolA C-terminal / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / Tol-Pal system, TolA / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Colicin-A / Tol-Pal system protein TolA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Citrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsLi, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Evidence That Colicin A Protein Binds to a Novel Binding Site of TolA Protein in Escherichia coli Periplasm.
Authors: Li, C. / Zhang, Y. / Vankemmelbeke, M. / Hecht, O. / Aleanizy, F.S. / Macdonald, C. / Moore, G.R. / James, R. / Penfold, C.N.
History
DepositionJan 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein tolA
B: Colicin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0673
Polymers19,9442
Non-polymers1221
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-6 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.497, 119.624, 30.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein tolA


Mass: 13140.814 Da / Num. of mol.: 1 / Fragment: TolA domain III, residues 302-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: tolA, cim, excC, lky, b0739, JW0729 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19934
#2: Protein Colicin-A


Mass: 6803.556 Da / Num. of mol.: 1 / Fragment: ColA, residues 53-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: caa, ColA / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04480
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M K2HPO4, 2.2 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-210.8726
SYNCHROTRONESRF ID14-420.9795
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJun 15, 2009
ADSC QUANTUM 315r2CCDMar 12, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1horizontally diffracting monochromatorSINGLE WAVELENGTHMx-ray1
2channel cut ESRF monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
20.97951
ReflectionResolution: 2.65→59.8 Å / Num. obs: 5238 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.098 / Rsym value: 0.129 / Net I/σ(I): 10.5
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.454 / % possible all: 98.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.65→59.8 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.857 / SU B: 12.681 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.928 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27263 234 4.5 %RANDOM
Rwork0.24385 ---
obs0.24518 4973 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.445 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--1.16 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.65→59.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 8 26 1087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221098
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9891495
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3625144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68325.95242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.88615170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.891153
X-RAY DIFFRACTIONr_chiral_restr0.1340.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022841
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5941.5718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1421152
X-RAY DIFFRACTIONr_scbond_it1.5293380
X-RAY DIFFRACTIONr_scangle_it2.4764.5342
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 12 -
Rwork0.274 363 -
obs--98.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.07730.57181.52272.21120.7032.378-0.04790.35920.0074-0.45450.0205-0.5973-0.1050.60090.02740.15690.01240.10180.17030.04090.221616.685229.24591.518
23.0768-0.2787-0.33531.75030.05710.17190.0726-0.02260.1453-0.0427-0.0153-0.1142-0.12630.0354-0.05730.1039-0.03070.02570.01340.0010.03071.6234.045514.6216
30.98440.130.44670.2263-0.24470.96370.032-0.1160.08030.1071-0.0390.0207-0.0162-0.0260.0070.0925-0.00880.00660.04760.0080.04158.499224.94817.367
40.1273-0.2738-0.65831.43752.85656.25870.01350.1094-0.0056-0.0877-0.07850.1436-0.0968-0.34290.0650.0673-0.0116-0.02180.12340.03420.11971.400918.18565.875
51.1630.22120.88810.05890.20180.7790.0150.0144-0.07290.0394-0.0004-0.00990.10220.0142-0.01470.085-0.00210.0240.04060.00810.04713.979724.994921.6472
63.197-0.8639-3.86140.25661.04594.70230.0860.03940.0796-0.0467-0.0204-0.0015-0.0918-0.038-0.06560.04080.0009-0.00580.0278-0.00080.04110.969724.58695.5973
71.9107-0.3556-0.15990.6152-0.68331.1067-0.003-0.08330.05920.03890.0331-0.0457-0.00980.0224-0.030.01230.0062-0.02170.0316-0.00570.043911.024823.66759.647
80.01970.0204-0.02140.0276-0.00730.0613-0.016-0.0257-0.0471-0.01280-0.06230.0440.08790.0160.13790.01150.00650.15330.00930.14544.63917.622212.0794
90.0093-0.00460.01560.0332-0.010.02870.00010.03570.0083-0.0395-0.0081-0.05580.01590.0620.0080.13640.00350.00430.14290.00380.13881.76138.53673.0594
100.1163-0.16680.26090.406-0.61351.27110.04640.10630.0027-0.157-0.05360.03380.04760.03210.00720.18150.0178-0.00930.1693-0.00420.151-5.81998.73078.0715
110.45330.28110.6180.34450.42421.4088-0.00930.1147-0.0348-0.11920.02690.0940.0405-0.0718-0.01760.1350.0143-0.02060.1336-0.01870.1431-3.207413.968618.4317
120.5403-0.6971-0.50911.6694-0.23532.23440.02320.11-0.1102-0.1123-0.010.13280.152-0.1117-0.01320.07070.00720.00490.0971-0.0150.09490.267115.970119.5001
130.2021-0.0340.06010.4959-0.77691.8915-0.02-0.2144-0.12410.21490.0942-0.017-0.0152-0.165-0.07420.2580.0194-0.01320.27870.05440.215-6.74345.153420.6471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A332 - 339
2X-RAY DIFFRACTION2A340 - 360
3X-RAY DIFFRACTION3A361 - 369
4X-RAY DIFFRACTION4A370 - 375
5X-RAY DIFFRACTION5A376 - 395
6X-RAY DIFFRACTION6A396 - 405
7X-RAY DIFFRACTION7A406 - 421
8X-RAY DIFFRACTION8B60 - 66
9X-RAY DIFFRACTION9B67 - 74
10X-RAY DIFFRACTION10B75 - 83
11X-RAY DIFFRACTION11B84 - 91
12X-RAY DIFFRACTION12B92 - 97
13X-RAY DIFFRACTION13B98 - 104

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