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- PDB-1k79: Ets-1(331-440)+GGAA duplex -

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Basic information

Entry
Database: PDB / ID: 1k79
TitleEts-1(331-440)+GGAA duplex
Components
  • C-ets-1 protein
  • DNA (5'-D(*CP*AP*CP*AP*TP*TP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*AP*AP*TP*GP*T)-3')
KeywordsTRANSCRIPTION/DNA / ETS domain / transcription factor / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding ...Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / DNA-binding transcription factor activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. ...Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / 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
DNA / DNA (> 10) / Protein C-ets-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGarvie, C.W. / Hagman, J. / Wolberger, C.
CitationJournal: Mol.Cell / Year: 2001
Title: Structural studies of Ets-1/Pax5 complex formation on DNA.
Authors: Garvie, C.W. / Hagman, J. / Wolberger, C.
History
DepositionOct 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*AP*AP*TP*GP*T)-3')
C: DNA (5'-D(*CP*AP*CP*AP*TP*TP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
E: DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*AP*AP*TP*GP*T)-3')
F: DNA (5'-D(*CP*AP*CP*AP*TP*TP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
A: C-ets-1 protein
D: C-ets-1 protein


Theoretical massNumber of molelcules
Total (without water)44,2806
Polymers44,2806
Non-polymers00
Water1,72996
1
B: DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*AP*AP*TP*GP*T)-3')
C: DNA (5'-D(*CP*AP*CP*AP*TP*TP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
A: C-ets-1 protein


Theoretical massNumber of molelcules
Total (without water)22,1403
Polymers22,1403
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*TP*AP*GP*TP*GP*CP*CP*GP*GP*AP*AP*AP*TP*GP*T)-3')
F: DNA (5'-D(*CP*AP*CP*AP*TP*TP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')
D: C-ets-1 protein


Theoretical massNumber of molelcules
Total (without water)22,1403
Polymers22,1403
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.740, 74.580, 79.140
Angle α, β, γ (deg.)90.00, 116.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 4649.033 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*CP*AP*TP*TP*TP*CP*CP*GP*GP*CP*AP*CP*T)-3')


Mass: 4504.936 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein C-ets-1 protein


Mass: 12985.833 Da / Num. of mol.: 2 / Fragment: ETS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ets-1 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27577
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4M-1.6M Sodium Citrate, 100mM Hepes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium citrate11
2Hepes11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 mMDNA1drop
21.4-1.6 Msodium citrate1reservoir
3100 mMHEPES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 6, 2001 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→17.05 Å / Num. all: 17326 / Num. obs: 17326 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.7 / % possible all: 58.7
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 58.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ets-1(331-440) bound to DNA from the Pax5(1-149)+Ets-1(331-440)+DNA complex

Resolution: 2.4→17.05 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1024028 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1723 10 %RANDOM
Rwork0.224 ---
all0.233 17300 --
obs0.233 17300 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0221 Å2 / ksol: 0.370139 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.92 Å20 Å2-2.43 Å2
2---5.47 Å20 Å2
3---0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→17.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 1214 0 96 3056
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 206 -
Rwork0.373 0 -
obs--64.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 17.1 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.228 / Rfactor Rfree: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.419 / Rfactor Rwork: 0.373

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