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- PDB-3tuo: Crystal structure of N-terminal domain of DNA-binding protein satb1 -

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Basic information

Entry
Database: PDB / ID: 3tuo
TitleCrystal structure of N-terminal domain of DNA-binding protein satb1
ComponentsDNA-binding protein SATB1
KeywordsDNA BINDING PROTEIN / DNA binding
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, ubiquitin-like oligomerisation domain / Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / 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 ...SATB, ubiquitin-like oligomerisation domain / Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / 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 / CUT domain / CUT domain / CUT domain profile. / CUT / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
DNA-binding protein SATB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.697 Å
AuthorsWang, Z. / Yang, X. / Long, J. / Shen, Y.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The structural basis for the oligomerization of the N-terminal domain of SATB1
Authors: Wang, Z. / Yang, X. / Chu, X. / Zhang, J. / Zhou, H. / Shen, Y. / Long, J.
History
DepositionSep 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: DNA-binding protein SATB1
B: DNA-binding protein SATB1
C: DNA-binding protein SATB1
D: DNA-binding protein SATB1


Theoretical massNumber of molelcules
Total (without water)46,6334
Polymers46,6334
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-37 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.895, 71.027, 153.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DNA-binding protein SATB1 / Special AT-rich sequence-binding protein 1


Mass: 11658.345 Da / Num. of mol.: 4 / Fragment: residues 71-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SATB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01826
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% polyethylene glycol 3350, 0.15M ammonium citrite dibasic, 4% polypropylene glycol P400, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9793
SYNCHROTRONSSRF BL17U20.9793
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 20, 2009
MARMOSAIC 225 mm CCD2CCDNov 23, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.697→50 Å / Num. all: 42483 / Num. obs: 42418 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.066 / Net I/σ(I): 24.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 3 / Num. unique all: 2982 / Rsym value: 0.19 / % possible all: 68.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.697→26.235 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8534 / SU ML: 0.24 / σ(F): 0.09 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2102 5.05 %RANDOM
Rwork0.1583 ---
obs0.1614 41595 93.46 %-
all-42483 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.824 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 104.04 Å2 / Biso mean: 33.4416 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1-4.7687 Å2-0 Å20 Å2
2---4.3479 Å2-0 Å2
3----0.4209 Å2
Refinement stepCycle: LAST / Resolution: 1.697→26.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 0 296 3277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053048
X-RAY DIFFRACTIONf_angle_d0.9264155
X-RAY DIFFRACTIONf_chiral_restr0.064494
X-RAY DIFFRACTIONf_plane_restr0.004525
X-RAY DIFFRACTIONf_dihedral_angle_d15.9421051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6972-1.73670.2129950.12411602169759
1.7367-1.78010.23691000.11622059215974
1.7801-1.82820.21991340.11172405253987
1.8282-1.8820.19961270.11592653278094
1.882-1.94270.21681580.11672659281797
1.9427-2.01210.23861490.12552743289298
2.0121-2.09260.20251430.13272784292799
2.0926-2.18780.19361410.13162735287699
2.1878-2.30310.2171340.14452799293399
2.3031-2.44730.20971410.142928132954100
2.4473-2.63610.23861440.15512801294599
2.6361-2.90110.22361470.154228162963100
2.9011-3.32020.20871670.169528543021100
3.3202-4.18030.20411670.15628793046100
4.1803-26.23860.21611550.17672891304695

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