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- PDB-4l5k: Crystal structure of the complex of DNA hexamer d(CGATCG) with Co... -

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Basic information

Entry
Database: PDB / ID: 4l5k
TitleCrystal structure of the complex of DNA hexamer d(CGATCG) with Coptisine
ComponentsDNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
KeywordsDNA / DRUG-DNA COMPLEX / Isoquinoline alkaloid
Function / homologyChem-KPT / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsFerraroni, M. / Bazzicalupi, C. / Gratteri, P.
CitationJournal: to be published
Title: Crystal structure of the complex of DNA hexamer d(CGATCG) with Coptisine
Authors: Ferraroni, M. / Bazzicalupi, C. / Gratteri, P.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,1302
Polymers1,8091
Non-polymers3201
Water543
1
A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,2594
Polymers3,6182
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area570 Å2
ΔGint-11 kcal/mol
Surface area2810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.581, 26.581, 77.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-101-

KPT

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-KPT / 6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium / Coptisine


Mass: 320.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14NO4 / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% MPD, 40 mM Na Cacodylate, 12 mM spermine tetra-HCl, 80 mM sodium chloride and 20 mM barium chloride, pH 6.0, vapor diffusion, sitting drop, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.542 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.7→14.78 Å / Num. obs: 558 / % possible obs: 97 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.99
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.99-3.160.7763.69187.9
3.16-3.370.1548.71198.5
3.37-3.620.11317.091100
3.62-3.940.14115.731100
3.94-4.350.11918.831100
4.35-4.940.06825.661100
4.94-5.850.06333.531100
5.85-7.570.05531.871100
7.570.0532.03186.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å14.69 Å
Translation3.5 Å14.69 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FT6

3ft6


Resolution: 2.71→14.78 Å / Cor.coef. Fo:Fc: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 28.317 / SU ML: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.2671 --
obs0.2671 558 98.59 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.273 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å21.06 Å2-0 Å2
2--2.11 Å2-0 Å2
3----6.85 Å2
Refinement stepCycle: LAST / Resolution: 2.71→14.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 24 3 147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.012163
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9221.48249
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.1070.218
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0287
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.4119.365163
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.706→2.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.812 32 -
Rfree-0 -
obs--96.97 %

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