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- PDB-4ocd: In and Out the minor groove: Interaction of an AT rich-DNA with t... -

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Basic information

Entry
Database: PDB / ID: 4ocd
TitleIn and Out the minor groove: Interaction of an AT rich-DNA with the CD27 drug
Componentsd(AAAATTTT)
KeywordsDNA / DNA minor groove binding drugs / all-AT DNA / dicationic drug / imidazoline drug
Function / homologyChem-MWB / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAcosta-Reyes, F.J. / Dardonville, C. / de Koning, H.P. / Natto, M. / Subirana, J.A. / Campos, J.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27
Authors: Acosta-Reyes, F.J. / Dardonville, C. / de Koning, H.P. / Natto, M. / Subirana, J.A. / Campos, J.L.
History
DepositionJan 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: d(AAAATTTT)
B: d(AAAATTTT)
C: d(AAAATTTT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2806
Polymers7,2743
Non-polymers1,0063
Water1,15364
1
A: d(AAAATTTT)
hetero molecules

A: d(AAAATTTT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5204
Polymers4,8492
Non-polymers6712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area680 Å2
ΔGint-6 kcal/mol
Surface area3160 Å2
MethodPISA
2
B: d(AAAATTTT)
C: d(AAAATTTT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5204
Polymers4,8492
Non-polymers6712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-7 kcal/mol
Surface area3120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.013, 78.013, 91.552
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

21B-214-

HOH

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Components

#1: DNA chain d(AAAATTTT)


Mass: 2424.641 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Chemical ChemComp-MWB / N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine / CD27


Mass: 335.406 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21N7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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

Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.25 mM DNA duplex, 0.75 mM CD27, 40 mM sodium cacodylate buffer pH 6.5, 8 mM MnCl2 , 0.5 mM spermine and 5% MPD equilibrated against a 30% MPD reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 288.15 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2013
RadiationMonochromator: Channel-cut Si(111), KB focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→39 Å / Num. obs: 10091 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Biso Wilson estimate: 59.64 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 30.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.1-2.216.850.5831433199.84
2.21-2.3510.380.494.6613671100
2.35-2.5113.050.279.121290199.96
2.51-2.7112.790.1514.481194199.9
2.71-2.9712.870.0727.71115199.98
2.97-3.3212.560.0342.171006199.42
3.32-3.8312.460.0364.47907199.9
3.83-4.7120.0374.68778199.73
4.7-6.6411.830.0375.19625199.34
6.64-3910.10.0274.71376198.22

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25103 480 4.8 %RANDOM
Rwork0.23614 ---
obs0.23682 9432 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.32 Å2
Baniso -1Baniso -2Baniso -3
1--3.21 Å2-1.61 Å20 Å2
2---3.21 Å20 Å2
3---10.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 483 75 64 622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.011635
X-RAY DIFFRACTIONr_bond_other_d0.0080.018348
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.281939
X-RAY DIFFRACTIONr_angle_other_deg7.2223813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02594
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02126
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.2955.9494
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.3096.208631
X-RAY DIFFRACTIONr_scbond_other7.3036.211632
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.8959.31940
X-RAY DIFFRACTIONr_long_range_B_refined13.34859.0132600
X-RAY DIFFRACTIONr_long_range_B_other13.42458.9742548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 31 -
Rwork0.437 622 -
obs--89.82 %

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