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- PDB-2f03: Crystal structure of tetrameric restriction endonuclease SfiI in ... -

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Basic information

Entry
Database: PDB / ID: 2f03
TitleCrystal structure of tetrameric restriction endonuclease SfiI in complex with cognate DNA (partial bound form)
Components
  • DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')
  • DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')
  • Type II restriction enzyme SfiI
KeywordsHydrolase/DNA / Type IIF restriction endonuclease / protein-DNA complex / deoxyribonuclease / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system
Similarity search - Function
Type II restriction enzyme SfiI, DNA-recognition domain / Type II restriction enzyme SfiI, multifunctional domain / Type II restriction enzyme SfiI / Restriction endonuclease, type II SfiI, domain 2 / Restriction endonuclease, type II SfiI, domain 1 / Type II restriction enzyme SfiI / ECO RV Endonuclease; Chain A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich ...Type II restriction enzyme SfiI, DNA-recognition domain / Type II restriction enzyme SfiI, multifunctional domain / Type II restriction enzyme SfiI / Restriction endonuclease, type II SfiI, domain 2 / Restriction endonuclease, type II SfiI, domain 1 / Type II restriction enzyme SfiI / ECO RV Endonuclease; Chain A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme SfiI
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.05 Å
AuthorsAggarwal, A.K. / Vanamee, E.S. / Viadiu, H
CitationJournal: Embo J. / Year: 2005
Title: A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
Authors: Vanamee, E.S. / Viadiu, H. / Kucera, R. / Dorner, L. / Picone, S. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionNov 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')
F: DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')
G: DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')
H: DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')
A: Type II restriction enzyme SfiI
C: Type II restriction enzyme SfiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3988
Polymers88,3186
Non-polymers802
Water2,000111
1
E: DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')
F: DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')
G: DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')
H: DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')
A: Type II restriction enzyme SfiI
C: Type II restriction enzyme SfiI
hetero molecules

E: DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')
F: DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')
G: DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')
H: DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')
A: Type II restriction enzyme SfiI
C: Type II restriction enzyme SfiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,79616
Polymers176,63612
Non-polymers1604
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)85.600, 85.600, 418.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Number of models2
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: x, x-y, 1/6-z.

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Components

#1: DNA chain DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3')


Mass: 6447.185 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3')


Mass: 6438.171 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein Type II restriction enzyme SfiI / Endonuclease SfiI / R.SfiI


Mass: 31273.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: E.coli
References: UniProt: O52512, type II site-specific deoxyribonuclease
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: pH 4.6-5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.928, 0.97931
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9281
20.979311
ReflectionResolution: 3.05→50 Å / Num. obs: 31321 / % possible obs: 99.7 %

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 3.05→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.293 1550 4.7 %
Rwork0.241 --
obs-31321 95.8 %
Solvent computationBsol: 34.984 Å2
Displacement parametersBiso mean: 38.301 Å2
Baniso -1Baniso -2Baniso -3
1--5.994 Å2-14.763 Å20 Å2
2---5.994 Å20 Å2
3---11.989 Å2
Refinement stepCycle: LAST / Resolution: 3.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 502 2 111 4912
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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