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- PDB-1sbx: Crystal structure of the Dachshund-homology domain of human SKI -

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Basic information

Entry
Database: PDB / ID: 1sbx
TitleCrystal structure of the Dachshund-homology domain of human SKI
ComponentsSki oncogene
KeywordsONCOPROTEIN / winged helix / forkhead
Function / homology
Function and homology information


nose morphogenesis / histone deacetylase inhibitor activity / myotube differentiation / lens morphogenesis in camera-type eye / negative regulation of Schwann cell proliferation / camera-type eye morphogenesis / olfactory bulb development / myelination in peripheral nervous system / Signaling by BMP / negative regulation of activin receptor signaling pathway ...nose morphogenesis / histone deacetylase inhibitor activity / myotube differentiation / lens morphogenesis in camera-type eye / negative regulation of Schwann cell proliferation / camera-type eye morphogenesis / olfactory bulb development / myelination in peripheral nervous system / Signaling by BMP / negative regulation of activin receptor signaling pathway / camera-type eye development / bone morphogenesis / embryonic limb morphogenesis / face morphogenesis / anterior/posterior axis specification / cardiac muscle cell proliferation / negative regulation of SMAD protein signal transduction / roof of mouth development / SMAD binding / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / positive regulation of DNA binding / skeletal muscle fiber development / negative regulation of fibroblast proliferation / transcription repressor complex / transforming growth factor beta receptor signaling pathway / cell motility / neural tube closure / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / retina development in camera-type eye / DNA-binding transcription factor binding / transcription regulator complex / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ski / : / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC family / Mlu1-box Binding Protein; DNA-binding Domain ...Ski / : / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC family / Mlu1-box Binding Protein; DNA-binding Domain / SAND-like domain superfamily / Putative DNA-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsWilson, J.J. / Malakhova, M. / Zhang, R. / Joachimiak, A. / Hegde, R.S.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of the Dachshund Homology Domain of human SKI
Authors: Wilson, J.J. / Malakhova, M. / Zhang, R. / Joachimiak, A. / Hegde, R.S.
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ski oncogene


Theoretical massNumber of molelcules
Total (without water)11,8671
Polymers11,8671
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.927, 46.633, 35.729
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ski oncogene / C-ski


Mass: 11867.272 Da / Num. of mol.: 1 / Fragment: Dachshund-homology domain of human SKI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKI / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P12755
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.82 Å3/Da / Density % sol: 32.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97834, 0.97852, 0.95372
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 3, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978341
20.978521
30.953721
ReflectionResolution: 1.5→50 Å / Num. all: 20103 / Num. obs: 19541 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 9.8 Å2 / Rsym value: 0.107
Reflection shellResolution: 1.5→1.55 Å / % possible all: 67.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→22.62 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 547143.35 / Data cutoff high rms absF: 547143.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1817 9.3 %RANDOM
Rwork0.17 ---
all0.184 20103 --
obs0.184 19541 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9922 Å2 / ksol: 0.387636 e/Å3
Displacement parametersBiso mean: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.23 Å2
2--0.58 Å20 Å2
3----1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.65→22.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms865 0 0 79 944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.214 281 8.9 %
Rwork0.202 2873 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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