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- PDB-3i5l: Allosteric Modulation of DNA by Small Molecules -

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Basic information

Entry
Database: PDB / ID: 3i5l
TitleAllosteric Modulation of DNA by Small Molecules
Components5'-D(*CP*CP*AP*GP*GP*(C38)P*CP*TP*GP*G)-3'
KeywordsDNA / Cyclic Polyamide / DNA Binder / Minor Groove Binder / PyIm Polyamide
Function / homologyChem-1P1 / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.18 Å
AuthorsChenoweth, D.M. / Dervan, P.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Allosteric modulation of DNA by small molecules
Authors: Chenoweth, D.M. / Dervan, P.B.
History
DepositionJul 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: 5'-D(*CP*CP*AP*GP*GP*(C38)P*CP*TP*GP*G)-3'
B: 5'-D(*CP*CP*AP*GP*GP*(C38)P*CP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7258
Polymers6,3442
Non-polymers1,3826
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-14 kcal/mol
Surface area3380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.500, 25.140, 29.090
Angle α, β, γ (deg.)66.53, 79.28, 79.57
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain 5'-D(*CP*CP*AP*GP*GP*(C38)P*CP*TP*GP*G)-3'


Mass: 3171.889 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid Phase Synthesis
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-1P1 / (22R,51R)-22,51-diamino-5,11,17,28,34,40,46,57-octamethyl-2,5,8,11,14,17,20,25,28,31,34,37,40,43,46,49,54,57,60,61,64,6 5-docosaazanonacyclo[54.2.1.1~4,7~.1~10,13~.1~16,19~.1~27,30~.1~33,36~.1~39,42~.1~45,48~]hexahexaconta-1(58),4(66),6,10( 65),12,16(64),18,27(63),29,33(62),35,39(61),41,45(60),47,56(59)-hexadecaene-3,9,15,21,26,32,38,44,50,55-decone / Cyclic Polyamide


Mass: 1181.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C52H60N24O10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 21% 2-methyl-2,4-pentanediol (MPD), 35 mM calcium acetate, 10 mM Tris pH 7.5 equilibrated in sitting drops against a reservoir of 35% MPD at 4 C. , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.175→26.472 Å / Num. obs: 19011 / Redundancy: 4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.5
Reflection shellResolution: 1.175→1.205 Å / Redundancy: 4 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 8.9 / % possible all: 90.16

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.18→26.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.816 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13764 1835 10.2 %RANDOM
Rwork0.09902 ---
obs0.103 16139 94.55 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 5.679 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.05 Å20.04 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.18→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 441 92 262 795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021587
X-RAY DIFFRACTIONr_bond_other_d0.0040.02232
X-RAY DIFFRACTIONr_angle_refined_deg2.5653896
X-RAY DIFFRACTIONr_angle_other_deg1.4813576
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_restr0.1210.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0370.02364
X-RAY DIFFRACTIONr_gen_planes_other0.020.0284
X-RAY DIFFRACTIONr_nbd_refined0.2380.2107
X-RAY DIFFRACTIONr_nbd_other0.2720.2362
X-RAY DIFFRACTIONr_nbtor_refined0.2380.2209
X-RAY DIFFRACTIONr_nbtor_other0.0890.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3760.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.220
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3640.286
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0820.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6681.55
X-RAY DIFFRACTIONr_mcbond_other1.2851.53
X-RAY DIFFRACTIONr_mcangle_it2.0227
X-RAY DIFFRACTIONr_scbond_it2.1633826
X-RAY DIFFRACTIONr_scangle_it2.6044.5889
X-RAY DIFFRACTIONr_rigid_bond_restr1.72531274
X-RAY DIFFRACTIONr_sphericity_free12.4063268
X-RAY DIFFRACTIONr_sphericity_bonded5.2253759
LS refinement shellResolution: 1.175→1.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.149 126 -
Rwork0.087 1138 -
obs--90.16 %

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