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- PDB-1pt3: Crystal structures of nuclease-ColE7 complexed with octamer DNA -

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Basic information

Entry
Database: PDB / ID: 1pt3
TitleCrystal structures of nuclease-ColE7 complexed with octamer DNA
Components
  • 5'-GCGATCGC-3'
  • Colicin E7
KeywordsHydrolase/DNA / HNH MOTIF / ENDONUCLEASE / COLICIN / PROTEIN-DNA COMPLEX / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


extrachromosomal circular DNA / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / metal ion binding
Similarity search - Function
Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily ...Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / HNH nucleases / HNH nuclease / His-Me finger superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHsia, K.C. / Chak, K.F. / Cheng, Y.S. / Ku, W.Y. / Yuan, H.S.
CitationJournal: STRUCTURE / Year: 2004
Title: DNA binding and degradation by the HNH protein ColE7.
Authors: Hsia, K.C. / Chak, K.F. / Liang, P.H. / Cheng, Y.S. / Ku, W.Y. / Yuan, H.S.
History
DepositionJun 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-GCGATCGC-3'
D: 5'-GCGATCGC-3'
G: 5'-GCGATCGC-3'
H: 5'-GCGATCGC-3'
E: 5'-GCGATCGC-3'
F: 5'-GCGATCGC-3'
A: Colicin E7
B: Colicin E7


Theoretical massNumber of molelcules
Total (without water)43,8898
Polymers43,8898
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.430, 46.470, 78.450
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S).

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Components

#1: DNA chain
5'-GCGATCGC-3'


Mass: 2427.605 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: This sequence occurs naturally in E. coli.
#2: Protein Colicin E7 / 3.1.-.-


Mass: 14661.624 Da / Num. of mol.: 2 / Fragment: residues 449-576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: COLE7 / Plasmid: PQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q47112, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 2.5 mM EDTA, 12.5 mM Tris-HCl (pH 7.5), 0.1 M Ammonium Formate, and 10 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.50
Components of the solutions
IDNameCrystal-IDSol-ID
1EDTA11
2Tris-HCl11
3Ammonium Formate11
4PEG 335011
5H2O11
6PEG 335012
7Ammonium Formate12
8H2O12
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22.5 mMEDTA1drop
312.5 mMTris-HCl1droppH7.5
40.1 Mammonium formate1drop
510 %PEG33501drop
60.2 Mammonium formate1reservoir
720 %PEG33501reservoir
81

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 15076 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 4.07 % / Biso Wilson estimate: 32.2 Å2 / Rsym value: 0.045 / Net I/σ(I): 36.4
Reflection shellResolution: 2.49→2.58 Å / Mean I/σ(I) obs: 7.8 / Rsym value: 0.241 / % possible all: 84.4
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 96.7 % / Num. measured all: 61443 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 83.2 % / Rmerge(I) obs: 0.236

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CEI

7cei


Resolution: 2.5→27.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 567313.87 / Data cutoff high rms absF: 567313.87 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1455 10.1 %RANDOM
Rwork0.216 ---
obs0.216 14389 95.3 %-
all-14389 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.96 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.81 Å20 Å2-0.96 Å2
2--9.19 Å20 Å2
3----15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 966 0 232 3262
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 188 8.6 %
Rwork0.301 2004 -
obs--88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.83

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