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- PDB-1sfu: Crystal structure of the viral Zalpha domain bound to left-handed... -

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Basic information

Entry
Database: PDB / ID: 1sfu
TitleCrystal structure of the viral Zalpha domain bound to left-handed Z-DNA
Components
  • 34L protein
  • 5'-D(*T*CP*GP*CP*GP*CP*G)-3'
KeywordsDNA Binding Protein/DNA / Protein-Z-DNA complex / DNA Binding Protein-DNA COMPLEX
Function / homology
Function and homology information


: / double-stranded RNA adenosine deaminase activity / peptidase activity / protein serine/threonine kinase activity / RNA binding
Similarity search - Function
: / Protein E3 / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...: / Protein E3 / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesYaba-like disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsHa, S.C. / Van Quyen, D. / Wu, C.A. / Lowenhaupt, K. / Rich, A. / Kim, Y.G. / Kim, K.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: A poxvirus protein forms a complex with left-handed Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound to DNA.
Authors: Ha, S.C. / Lokanath, N.K. / Van Quyen, D. / Wu, C.A. / Lowenhaupt, K. / Rich, A. / Kim, Y.G. / Kim, K.K.
History
DepositionFeb 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / database_2
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'-D(*T*CP*GP*CP*GP*CP*G)-3'
D: 5'-D(*T*CP*GP*CP*GP*CP*G)-3'
A: 34L protein
B: 34L protein


Theoretical massNumber of molelcules
Total (without water)21,6734
Polymers21,6734
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.203, 92.452, 48.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 2114.398 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein 34L protein


Mass: 8722.137 Da / Num. of mol.: 2 / Fragment: N-terminal Zalpha domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yaba-like disease virus / Genus: Yatapoxvirus / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9DHS8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.95 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1-1.1 M lithium sulfate, 2-4 mM magnesium chloride, 25 mM cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1lithium sulfate11
2magnesium chloride11
3cacodylate11
4H2O11
5lithium sulfate12
6magnesium chloride12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9201 / Wavelength: 0.9203, 0.9159
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92011
20.92031
30.91591
ReflectionResolution: 2→50 Å / Num. obs: 15772
Reflection shellResolution: 2→2.07 Å / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2704 1539 9.6 %random
Rwork0.2375 ---
all-15970 --
obs-15266 95.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.017 Å20 Å20 Å2
2--5.277 Å20 Å2
3----4.259 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 240 0 170 1542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_angle_deg1.1844

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