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- PDB-8t4n: DB1976 Bound to the DNA Sequence 5'-CGCGAATTCGCG-3 -

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Basic information

Entry
Database: PDB / ID: 8t4n
TitleDB1976 Bound to the DNA Sequence 5'-CGCGAATTCGCG-3
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / ETS family / ETS / PU.1 / diamidine / minor groove binder
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsTerrell, J.R. / Poon, G.M.K. / Wilson, W.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL155178 United States
National Science Foundation (NSF, United States)MCB2028902 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137160 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
CitationJournal: To Be Published
Title: Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders
Authors: Terrell, J.R. / Paul, A. / Ogbonna, E.N. / Farahat, A.A. / Poon, G.M.K. / Wilson, W.D.
History
DepositionJun 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7743
Polymers7,3272
Non-polymers4471
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.442, 41.286, 65.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 12)
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Label seq-ID: 1 - 2

Dom-IDAuth asym-IDLabel asym-IDAuth seq-ID
d_1AA1 - 2
d_2BB13 - 14

NCS oper: (Code: givenMatrix: (0.746581374184, -0.66349468731, -0.048898380684), (-0.664230094472, -0.747526477895, 0.00159575839863), (-0.0376116115072, 0.0312884125231, -0.998802483938)Vector: 18. ...NCS oper: (Code: given
Matrix: (0.746581374184, -0.66349468731, -0.048898380684), (-0.664230094472, -0.747526477895, 0.00159575839863), (-0.0376116115072, 0.0312884125231, -0.998802483938)
Vector: 18.2680653931, 47.4926105238, 17.5080709287)

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-Y5U / (2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide)


Mass: 447.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16N8Se / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40 mM Sodium Cacodylate pH=6.0, 12 mM Spermine tetrahydrochloride, 12 mM NaCl, 80 mM KCl, 10% MPD mixed in a 1:1 ratio with 1 mM DNA duplex annealed in the presence of ligand. Well solution ...Details: 40 mM Sodium Cacodylate pH=6.0, 12 mM Spermine tetrahydrochloride, 12 mM NaCl, 80 mM KCl, 10% MPD mixed in a 1:1 ratio with 1 mM DNA duplex annealed in the presence of ligand. Well solution for vapor diffusion was 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 18, 2022
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.79→34.96 Å / Num. obs: 6849 / % possible obs: 98.52 % / Redundancy: 7.6 % / Biso Wilson estimate: 38.62 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03026 / Rpim(I) all: 0.01215 / Rrim(I) all: 0.03272 / Net I/σ(I): 31.49
Reflection shellResolution: 1.79→1.854 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.5558 / Mean I/σ(I) obs: 4.31 / Num. unique obs: 675 / CC1/2: 0.963 / CC star: 0.99 / Rpim(I) all: 0.2102 / Rrim(I) all: 0.5952 / % possible all: 99.56

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→34.96 Å / SU ML: 0.2159 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2471 684 10 %
Rwork0.2171 6159 -
obs0.2203 6843 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.34 Å2
Refinement stepCycle: LAST / Resolution: 1.79→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 29 32 547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134577
X-RAY DIFFRACTIONf_angle_d1.6535885
X-RAY DIFFRACTIONf_chiral_restr0.076694
X-RAY DIFFRACTIONf_plane_restr0.016130
X-RAY DIFFRACTIONf_dihedral_angle_d29.1857259
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.6976999752 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.930.31971340.27051210X-RAY DIFFRACTION99.7
1.93-2.120.34051370.2821230X-RAY DIFFRACTION99.78
2.12-2.430.30561370.26881228X-RAY DIFFRACTION100
2.43-3.060.33061380.26541241X-RAY DIFFRACTION99.93
3.06-34.960.19411380.18211250X-RAY DIFFRACTION93.66
Refinement TLS params.Method: refined / Origin x: 14.8860800471 Å / Origin y: 21.4183642983 Å / Origin z: 8.66829109742 Å
111213212223313233
T0.369429306673 Å2-0.000841703834707 Å20.0253852295606 Å2-0.353688616218 Å2-0.0317196595566 Å2--0.349393873721 Å2
L2.16126734414 °2-0.0573354123764 °20.941323143557 °2-1.53038453839 °22.58177943405 °2--4.82455390492 °2
S0.225425722544 Å °-0.166610832272 Å °0.178270556634 Å °-0.200782708001 Å °-0.000273126726086 Å °-0.0566993626284 Å °-0.328952975787 Å °-0.403844026203 Å °-0.196963539717 Å °
Refinement TLS groupSelection details: all

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