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- PDB-4x0g: Structure of Bsg25A binding with DNA -

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Basic information

Entry
Database: PDB / ID: 4x0g
TitleStructure of Bsg25A binding with DNA
Components
  • Blastoderm-specific gene 25A
  • DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
KeywordsDNA BINDING PROTEIN/DNA / Bsg25A / Elba1 / ben. DNA-binding / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / embryonic development via the syncytial blastoderm / chromatin insulator sequence binding / chromatin silencing complex / sequence-specific DNA binding / nucleus
Similarity search - Function
BEN domain / BEN domain / BEN domain / BEN domain profile. / BEN / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / Early boundary activity protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2065 Å
AuthorsRen, A.
CitationJournal: Genes Dev. / Year: 2015
Title: Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family.
Authors: Dai, Q. / Ren, A. / Westholm, J.O. / Duan, H. / Patel, D.J. / Lai, E.C.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.d_res_high / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blastoderm-specific gene 25A
B: Blastoderm-specific gene 25A
C: Blastoderm-specific gene 25A
D: Blastoderm-specific gene 25A
E: DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
F: DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
G: DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
H: DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,69211
Polymers64,5158
Non-polymers1773
Water181
1
A: Blastoderm-specific gene 25A
B: Blastoderm-specific gene 25A
E: DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
F: DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3766
Polymers32,2574
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-41 kcal/mol
Surface area14620 Å2
MethodPISA
2
C: Blastoderm-specific gene 25A
D: Blastoderm-specific gene 25A
G: DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
H: DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3175
Polymers32,2574
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-41 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.550, 92.550, 62.998
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Blastoderm-specific gene 25A / RE24665p


Mass: 12138.113 Da / Num. of mol.: 4 / Fragment: UNP residues 250-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Bsg25A, CG12205, Dmel_CG12205 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VR17
#2: DNA chain
DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')


Mass: 3990.622 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M NaOAc pH 4.6, 25% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 9889 / % possible obs: 99.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 7.1
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IX7

4ix7


Resolution: 3.2065→40.075 Å / FOM work R set: 0.7609 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 474 4.81 %
Rwork0.2282 9389 -
obs0.2307 9863 99.8 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.68 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 116.44 Å2 / Biso mean: 59.02 Å2 / Biso min: 31.28 Å2
Baniso -1Baniso -2Baniso -3
1-3.7508 Å20 Å2-0 Å2
2--3.7508 Å2-0 Å2
3----7.5015 Å2
Refinement stepCycle: final / Resolution: 3.2065→40.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 1060 12 1 4397
Biso mean--61.71 36.63 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024577
X-RAY DIFFRACTIONf_angle_d0.6386413
X-RAY DIFFRACTIONf_chiral_restr0.035750
X-RAY DIFFRACTIONf_plane_restr0.003637
X-RAY DIFFRACTIONf_dihedral_angle_d18.3691808
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2065-3.67030.29071450.259831283273
3.6703-4.62310.26251740.218531343308
4.6231-40.07840.28211550.218731273282

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