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- PDB-2fhz: Molecular Basis of Inhibition of the Ribonuclease Activity in Col... -

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Basic information

Entry
Database: PDB / ID: 2fhz
TitleMolecular Basis of Inhibition of the Ribonuclease Activity in Colicin E5 by Its Cognate Immunity Protein
Components
  • Colicin-E5
  • Colicin-E5 immunity protein
KeywordsIMMUNE SYSTEM / HYDROLASE / Protein-Protein Complex / Inhibition of Ribonuclease
Function / homology
Function and homology information


bacteriocin immunity / RNA nuclease activity / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium
Similarity search - Function
Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase - #30 / Colicin-E5 immunity protein / ImmE5 superfamily / Colicin-E5 Imm protein / Colicin E5 C-terminal ribonuclease domain (CRD) / Colicin E5 ribonuclease domain / Colicin E5 ribonuclease domain superfamily / Colicin E5 ribonuclease domain / Colicin D/E5 nuclease domain superfamily / YaeB-like fold ...Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase - #30 / Colicin-E5 immunity protein / ImmE5 superfamily / Colicin-E5 Imm protein / Colicin E5 C-terminal ribonuclease domain (CRD) / Colicin E5 ribonuclease domain / Colicin E5 ribonuclease domain superfamily / Colicin E5 ribonuclease domain / Colicin D/E5 nuclease domain superfamily / YaeB-like fold / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Colicin-E5 immunity protein / Colicin-E5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å
AuthorsLin, Y.L. / Huang, R.H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Molecular basis of inhibition of the ribonuclease activity in colicin e5 by its cognate immunity protein
Authors: Luna-Chavez, C. / Lin, Y.L. / Huang, R.H.
History
DepositionDec 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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-E5 immunity protein
B: Colicin-E5


Theoretical massNumber of molelcules
Total (without water)24,3002
Polymers24,3002
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-3 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.790, 73.640, 110.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Colicin-E5 immunity protein / ImmE5 / Microcin-E5 immunity protein


Mass: 12303.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: imm / Plasmid: PLM1-ColE5-Imm5 from PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13476
#2: Protein Colicin-E5


Mass: 11996.320 Da / Num. of mol.: 1 / Fragment: residues 74-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: col / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P18000, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 % saturated ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9793
SYNCHROTRONAPS 14-BM-D20.9793, 0.9791, 0.9537
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 7, 2003
MARRESEARCH2CCDNov 12, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2YALE MIRRORSMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97911
30.95371
ReflectionResolution: 1.15→25 Å / Num. all: 89161 / Num. obs: 82619 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.034 / Rsym value: 0.025 / Net I/σ(I): 20.1
Reflection shellResolution: 1.15→1.2 Å / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 9.1 / Rsym value: 0.191 / % possible all: 82.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.15→25 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 6733 -RANDOM
Rwork0.195 ---
all0.197 89161 --
obs0.197 82619 92.7 %-
Refinement stepCycle: LAST / Resolution: 1.15→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 0 250 1822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0044
X-RAY DIFFRACTIONc_angle_deg1.296
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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