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- PDB-1tfo: Ribonuclease from Escherichia coli complexed with its inhibitor p... -

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Basic information

Entry
Database: PDB / ID: 1tfo
TitleRibonuclease from Escherichia coli complexed with its inhibitor protein
Components
  • Colicin D
  • Colicin D immunity protein
KeywordsTOXIN/TOXIN INHIBITOR / PROTEIN-PROTEIN COMPLEX / TOXIN-TOXIN INHIBITOR 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 / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsYajima, S. / Nakanishi, K. / Takahashi, K. / Ogawa, T. / Kezuka, Y. / Hidaka, M. / Nonaka, T. / Ohsawa, K. / Masaki, H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Relation between tRNase activity and the structure of colicin D according to X-ray crystallography
Authors: Yajima, S. / Nakanishi, K. / Takahashi, K. / Ogawa, T. / Hidaka, M. / Kezuka, Y. / Nonaka, T. / Ohsawa, K. / Masaki, H.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,5132
Polymers22,5132
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.171, 56.171, 149.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: Protein Colicin D


Mass: 11881.298 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CDA / Production host: Escherichia coli (E. coli) / References: UniProt: P17998
#2: Protein Colicin D immunity protein / ImmD / Microcin D immunity protein


Mass: 10631.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Inhibitor protein / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CDI / Production host: Escherichia coli (E. coli) / References: UniProt: P11899
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.67 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, glycerol, DTT, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 26, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→38.4 Å / Num. all: 11401 / Num. obs: 11367 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→38.4 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.309 568 RANDOM
Rwork0.258 --
all0.294 11401 -
obs0.269 11367 -
Refinement stepCycle: LAST / Resolution: 2.3→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 0 28 1561
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2

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