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- PDB-4ix7: Crystal Structure of the insv-BEN domain complexed to its DNA tar... -

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Basic information

Entry
Database: PDB / ID: 4ix7
TitleCrystal Structure of the insv-BEN domain complexed to its DNA target site
Components
  • 5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3'
  • RE55538p
KeywordsDNA BINDING PROTEIN/DNA / BEN domain / transcriptional repressor / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


chromatin insulator sequence binding / negative regulation of Notch signaling pathway / positive regulation of neuron differentiation / transcription corepressor activity / sequence-specific DNA binding / negative regulation of DNA-templated transcription / nucleus
Similarity search - Function
BEN domain-containing protein 6 / BEN domain / BEN domain / BEN domain / BEN domain profile. / BEN / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein insensitive
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.581 Å
AuthorsRen, A. / Serganov, A. / Patel, D.J.
CitationJournal: Genes Dev. / Year: 2013
Title: The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors.
Authors: Dai, Q. / Ren, A. / Westholm, J.O. / Serganov, A.A. / Patel, D.J. / Lai, E.C.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3'
D: 5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3'
A: RE55538p
B: RE55538p


Theoretical massNumber of molelcules
Total (without water)34,0904
Polymers34,0904
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-34 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.382, 75.464, 89.809
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: DNA chain 5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3'


Mass: 3990.622 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein RE55538p


Mass: 13054.505 Da / Num. of mol.: 2 / Fragment: Insv-BEN domain (UNP residues 251-365)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3227, insensitive, insv / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SYK5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 26% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 41090 / Num. obs: 41021 / % possible obs: 99.8 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 59.6
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 4 / Rsym value: 0.712 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.581→39.063 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2061 5.02 %
Rwork0.1894 --
obs0.1908 41021 99.84 %
all-41090 -
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.434 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0978 Å2-0 Å2-0 Å2
2--4.2616 Å2-0 Å2
3----1.1638 Å2
Refinement stepCycle: LAST / Resolution: 1.581→39.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 530 0 280 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062441
X-RAY DIFFRACTIONf_angle_d1.1273420
X-RAY DIFFRACTIONf_dihedral_angle_d18.269981
X-RAY DIFFRACTIONf_chiral_restr0.059399
X-RAY DIFFRACTIONf_plane_restr0.004349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.581-1.6180.25891510.22062524X-RAY DIFFRACTION100
1.618-1.65850.27371430.20572543X-RAY DIFFRACTION100
1.6585-1.70330.20421150.19312590X-RAY DIFFRACTION100
1.7033-1.75350.21481480.1892567X-RAY DIFFRACTION100
1.7535-1.810.21921460.19132579X-RAY DIFFRACTION100
1.81-1.87470.24181150.19362561X-RAY DIFFRACTION100
1.8747-1.94980.241410.19962581X-RAY DIFFRACTION100
1.9498-2.03850.25061340.20982583X-RAY DIFFRACTION100
2.0385-2.1460.21681430.19632583X-RAY DIFFRACTION100
2.146-2.28040.23231220.18782612X-RAY DIFFRACTION100
2.2804-2.45650.22971390.20242577X-RAY DIFFRACTION100
2.4565-2.70360.23531260.21052650X-RAY DIFFRACTION100
2.7036-3.09470.22651620.20512600X-RAY DIFFRACTION100
3.0947-3.89850.19811390.17332665X-RAY DIFFRACTION100
3.8985-39.07520.18271370.16862745X-RAY DIFFRACTION98

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