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- PDB-1z63: Sulfolobus solfataricus SWI2/SNF2 ATPase core in complex with dsDNA -

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Basic information

Entry
Database: PDB / ID: 1z63
TitleSulfolobus solfataricus SWI2/SNF2 ATPase core in complex with dsDNA
Components
  • 5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3'
  • 5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3'
  • Helicase of the snf2/rad54 family
KeywordsHYDROLASE/DNA complex / protein-DNA complex / HYDROLASE-DNA complex COMPLEX
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity / ATP-dependent activity, acting on DNA / helicase activity / DNA binding / ATP binding
Similarity search - Function
Helicase SWF/SNF-related / SNF2 Helicase protein / SWI2/SNF2 ATPases, N-terminal domain / Tandem AAA-ATPase domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helicase conserved C-terminal domain ...Helicase SWF/SNF-related / SNF2 Helicase protein / SWI2/SNF2 ATPases, N-terminal domain / Tandem AAA-ATPase domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Helicase of the snf2/rad54 family (Carboxy end), hypothetical / Helicase of the snf2/rad54 family (Amino end), hypothetical
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDuerr, H. / Koerner, C. / Mueller, M. / Hickmann, V. / Hopfner, K.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA.
Authors: Durr, H. / Korner, C. / Muller, M. / Hickmann, V. / Hopfner, K.P.
History
DepositionMar 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Experimental preparation
Revision 1.4Aug 23, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3'
D: 5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3'
E: 5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3'
F: 5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3'
A: Helicase of the snf2/rad54 family
B: Helicase of the snf2/rad54 family


Theoretical massNumber of molelcules
Total (without water)145,9226
Polymers145,9226
Non-polymers00
Water0
1
C: 5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3'
D: 5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3'
A: Helicase of the snf2/rad54 family


Theoretical massNumber of molelcules
Total (without water)72,9613
Polymers72,9613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3'
F: 5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3'
B: Helicase of the snf2/rad54 family


Theoretical massNumber of molelcules
Total (without water)72,9613
Polymers72,9613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.931, 83.737, 106.390
Angle α, β, γ (deg.)90.00, 109.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3'


Mass: 7759.107 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3'


Mass: 7592.886 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein Helicase of the snf2/rad54 family


Mass: 57609.016 Da / Num. of mol.: 2 / Fragment: residues 407-902
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97XQ5, UniProt: Q97XQ7*PLUS

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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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG3350, Magnesiumformate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG335011
2Magnesiumformate11
3PEG335012
4Magnesiumformate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 52560 / Num. obs: 52560 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.2 Å / % possible all: 72.1

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Processing

Software
NameClassification
HKL-2000data collection
XDSdata reduction
AMoREphasing
CNSrefinement
HKL-2000data reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 1401 random
Rwork0.233 --
obs0.233 28481 -
all-28897 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7568 1586 0 0 9154

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