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- PDB-2o49: Crystal Structure of the N-terminal CUT domain of SATB1 Bound to ... -

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Basic information

Entry
Database: PDB / ID: 2o49
TitleCrystal Structure of the N-terminal CUT domain of SATB1 Bound to Matrix Attachment Region DNA
Components
  • DNA (5'-D(*DGP*DCP*DAP*DTP*DAP*DTP*DAP*DTP*DTP*DAP*DGP*DC)-3')
  • DNA (5'-D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3')
  • DNA-binding protein SATB1
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / transcription / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / chromatin organization / double-stranded DNA binding / sequence-specific DNA binding / nuclear body ...Apoptotic cleavage of cellular proteins / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / chromatin organization / double-stranded DNA binding / sequence-specific DNA binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
SATB, CUT1-like DNA-binding domain / SATB, ubiquitin-like oligomerisation domain / SATB, CUTL domain superfamily / SATB, ULD domain superfamily / DNA-binding protein SATB1/SATB2 / Ubiquitin-like oligomerisation domain of SATB / CUT1-like DNA-binding domain of SATB / Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / CUT domain ...SATB, CUT1-like DNA-binding domain / SATB, ubiquitin-like oligomerisation domain / SATB, CUTL domain superfamily / SATB, ULD domain superfamily / DNA-binding protein SATB1/SATB2 / Ubiquitin-like oligomerisation domain of SATB / CUT1-like DNA-binding domain of SATB / Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / CUT domain / CUT domain / CUT domain profile. / CUT / Homeodomain / lambda repressor-like DNA-binding domains / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding protein SATB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYamasaki, K. / Akiba, T. / Harata, K.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.
Authors: Yamasaki, K. / Akiba, T. / Yamasaki, T. / Harata, K.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3')
C: DNA (5'-D(*DGP*DCP*DAP*DTP*DAP*DTP*DAP*DTP*DTP*DAP*DGP*DC)-3')
A: DNA-binding protein SATB1


Theoretical massNumber of molelcules
Total (without water)18,2753
Polymers18,2753
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.659, 36.997, 41.248
Angle α, β, γ (deg.)71.60, 83.92, 71.07
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain DNA (5'-D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3')


Mass: 3661.416 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DGP*DCP*DAP*DTP*DAP*DTP*DAP*DTP*DTP*DAP*DGP*DC)-3')


Mass: 3661.416 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA-binding protein SATB1 / Special AT-rich sequence-binding protein 1


Mass: 10952.381 Da / Num. of mol.: 1 / Fragment: N-terminal CUT domain (residues 368-452)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01826
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.23 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 20000, 0.05M TrisHCl, 0.01M magnesium chloride, 20% ethylene glycol, pH 8.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2000011
2TrisHCl11
3magnesium chloride11
4ethylene glycol11
5HOH11
6PEG 2000012
7TrisHCl12
8magnesium chloride12
9HOH12

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.64 Å / Num. obs: 9632 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1571 / % possible all: 55.2

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Processing

Software
NameVersionClassification
SMARTdata collection
CNS1.1refinement
SAINTPLUSdata reduction
SCALAdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YSE

1yse


Resolution: 2→19.57 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 578429.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 993 10.3 %RANDOM
Rwork0.212 ---
obs0.212 9613 90.3 %-
all-10638 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.906 Å2 / ksol: 0.646403 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1-7.81 Å26.73 Å21.35 Å2
2---5.87 Å22.28 Å2
3----1.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms696 486 0 75 1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.08
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 113 10.8 %
Rwork0.268 935 -
obs--59 %
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

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