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- PDB-1skn: THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDIN... -

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Basic information

Entry
Database: PDB / ID: 1skn
TitleTHE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF
Components
  • DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3')
  • DNA (5'-D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)-3')
  • DNA-BINDING DOMAIN OF SKN-1
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


: / positive regulation of cellular response to manganese ion / : / response to paraquat / Factors involved in megakaryocyte development and platelet production / positive regulation of cellular response to oxidative stress / : / mesendoderm development / endodermal cell fate specification / multicellular organism development ...: / positive regulation of cellular response to manganese ion / : / response to paraquat / Factors involved in megakaryocyte development and platelet production / positive regulation of cellular response to oxidative stress / : / mesendoderm development / endodermal cell fate specification / multicellular organism development / embryonic digestive tract development / embryonic pattern specification / response to superoxide / cell fate specification / Hsp70 protein binding / determination of adult lifespan / RNA polymerase II transcription regulatory region sequence-specific DNA binding / regulation of translation / response to heat / response to oxidative stress / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / host cell nucleus / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Transcription Factor Skn-1; Chain P / Transcription factor, Skn-1-like, DNA-binding domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein skinhead-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsRupert, P.B. / Daughdrill, G.W. / Bowerman, B. / Matthews, B.W.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: A new DNA-binding motif in the Skn-1 binding domain-DNA complex.
Authors: Rupert, P.B. / Daughdrill, G.W. / Bowerman, B. / Matthews, B.W.
History
DepositionMar 30, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)-3')
B: DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3')
P: DNA-BINDING DOMAIN OF SKN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4044
Polymers20,1743
Non-polymers2291
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.130, 93.390, 53.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11P-16-

LDA

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Components

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


Mass: 4528.961 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3')


Mass: 4649.033 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA-BINDING DOMAIN OF SKN-1 / DNA-BINDING DOMAIN OF TRANSCRIPTION FACTOR SKN-1


Mass: 10996.467 Da / Num. of mol.: 1 / Fragment: BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Cellular location: NUCLEUS / Gene: SKN-1 / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P34707
#4: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / LAURYL DIMETHYLAMINE-OXIDE


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Water ChemComp-HOH / water / WATER


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.5 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 8% PEG 1000 50 MM BIS-TRIS, PH 6.0, 100-150 MM LICL, 2MM LDAO., VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 100011
2LICL11
3BIS-TRIS11
4LDAO11
5PEG 100012
6LICL12
7BIS-TRIS12
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMprotein1drop
20.55 mM5'-15mer1drop
30.55 mM3'-15mer 1drop
450 mM1dropLiCl
52 mMN-lauryl-N,N-dimethylamine-N-oxide1drop
67-8 %PEG10001reservoir
7150 mM1reservoirLiCl
850 mMBis-Tris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 7202 / % possible obs: 94.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.116 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
TNTrefinement
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT
Details: THE SHORT CONTACTS LISTED IN REMARK 500 ARE THE RESULT OF THE LAURYLDIMETHYLAMINEOXIDE (LDA) MOLECULE MODELED ON A TWO-FOLD AXIS AT HALF OCCUPANCY. THIS LDA MOLECULE WAS EXCLUDED FROM MAKING ...Details: THE SHORT CONTACTS LISTED IN REMARK 500 ARE THE RESULT OF THE LAURYLDIMETHYLAMINEOXIDE (LDA) MOLECULE MODELED ON A TWO-FOLD AXIS AT HALF OCCUPANCY. THIS LDA MOLECULE WAS EXCLUDED FROM MAKING BAD CONTACTS WITH A SYMMETRY-RELATED COPY OF ITSELF IN THE TNT REFINEMENT PROTOCOL.
RfactorNum. reflection% reflectionSelection details
Rfree0.337 752 10 %RANDOM
Rwork0.22 ---
all0.24 7202 --
obs0.24 6450 97.5 %-
Solvent computationSolvent model: TNT 5F / Bsol: 110 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms610 609 16 28 1263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.7
X-RAY DIFFRACTIONt_dihedral_angle_d21.1
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.022
X-RAY DIFFRACTIONt_gen_planes0.02
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg21.1
X-RAY DIFFRACTIONt_plane_restr0.02

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