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- PDB-1v74: Structure of the E. coli colicin D bound to its immunity protein ImmD -

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Basic information

Entry
Database: PDB / ID: 1v74
TitleStructure of the E. coli colicin D bound to its immunity protein ImmD
Components
  • Colicin D
  • Colicin D immunity protein
KeywordsANTIBIOTIC/IMMUNE SYSTEM / colicin D - ImmD complex / cytotoxicity / transfer RNase / protein-protein inhibition / ANTIBIOTIC-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / RNA nuclease activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Colicin D / Nuclear Transport Factor 2; Chain: A, - #200 / Colicin D immunity protein domain / Colicin D superfamily / Bacterial self-protective colicin-like immunity / Colicin D, C-terminal / Colicin D, C-terminal domain superfamily / Colicin D / Colicin D/E5 nuclease domain superfamily / S-type Pyocin ...Colicin D / Nuclear Transport Factor 2; Chain: A, - #200 / Colicin D immunity protein domain / Colicin D superfamily / Bacterial self-protective colicin-like immunity / Colicin D, C-terminal / Colicin D, C-terminal domain superfamily / Colicin D / Colicin D/E5 nuclease domain superfamily / S-type Pyocin / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / Nuclear Transport Factor 2; Chain: A, / Four Helix Bundle (Hemerythrin (Met), subunit A) / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Colicin-D immunity protein / Colicin-D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGraille, M. / Mora, L. / Buckingham, R.H. / van Tilbeurgh, H. / de Zamaroczy, M.
CitationJournal: Embo J. / Year: 2004
Title: Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein
Authors: Graille, M. / Mora, L. / Buckingham, R.H. / Van Tilbeurgh, H. / De Zamaroczy, M.
History
DepositionDec 10, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 3, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Colicin D
B: Colicin D immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6313
Polymers22,3922
Non-polymers2381
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.057, 62.057, 147.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is present in the asymetric unit

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Components

#1: Protein Colicin D


Mass: 12320.763 Da / Num. of mol.: 1 / Fragment: colicin D catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pColD-CA23 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P17998
#2: Protein Colicin D immunity protein / Microcin D immunity protein


Mass: 10071.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pJF129 / Production host: Escherichia coli (E. coli) / References: UniProt: P11899
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.2161.37
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop830% PEG 400, 0.2M MgSO4, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop6.524% PEG 8000, 0.1M Na citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.99 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.98→99 Å / Num. all: 273269 / Num. obs: 20818 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.058 / Net I/σ(I): 18.9
Reflection shellResolution: 1.98→2.02 Å / Mean I/σ(I) obs: 1.6 / Num. unique all: 1184 / Rsym value: 0.278 / % possible all: 86.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.234 930 RANDOM
Rwork0.194 --
all-20299 -
obs-19396 -
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 16 195 1780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.266 139 -
Rwork0.23 --
obs-2950 89.5 %

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