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- PDB-4d9y: The crystal structure of Chelerythrine bound to DNA d(CGTACG) -

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Basic information

Entry
Database: PDB / ID: 4d9y
TitleThe crystal structure of Chelerythrine bound to DNA d(CGTACG)
ComponentsDNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / DRUG-DNA COMPLEX / DOUBLE HELIX
Function / homologyChem-CTI / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsFerraroni, M. / Bazzicalupi, C. / Gratteri, P. / Bilia, A.R.
CitationJournal: To be Published
Title: The crystal structure of Chelerythrine bound to DNA d(CGTACG)
Authors: Ferraroni, M. / Bazzicalupi, C. / Gratteri, P. / Bilia, A.R.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Refinement description
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_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: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
C: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6256
Polymers7,2374
Non-polymers3882
Water19811
1
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0074
Polymers3,6182
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-6 kcal/mol
Surface area2720 Å2
MethodPISA
2
C: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6182
Polymers3,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-2 kcal/mol
Surface area2640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.231, 30.231, 119.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 1809.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic DNA
#2: Chemical ChemComp-CTI / 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium / chelerythrine


Mass: 348.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18NO4 / Comment: inhibitor, alkaloid*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5
Details: MPD, MgCl2, NaCl, KCL, spermine, pH 6.5, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: PILATUS 2M / Detector: CCD / Date: Mar 13, 2011
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 4087 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 46.83 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.39
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.230.2265.34197.8
2.23-2.380.1877.62199.7
2.38-2.570.11712.23198.9
2.57-2.810.11114.29199
2.81-3.140.09216.98199.4
3.14-3.630.08918.84199.3
3.63-4.430.08519.33199.5
4.43-6.230.07818.79199.3
6.23-300.08317.57197.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å26.17 Å
Translation3.5 Å26.17 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
SHELXrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NP6

3np6


Resolution: 2.1→20 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Crystal was merohedrally twinned with a fraction of 0.46 and twin law -h, -k, l
RfactorNum. reflection% reflectionSelection details
Rfree0.314 209 -Reflections were chosen in thin resolution shells
Rwork0.2196 ---
obs-4087 93.9 %-
Displacement parametersBiso mean: 54.1262 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 450 27 11 488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.005
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 2.1→2.19 Å /
Rfactor% reflection
Rwork0.373 -
obs-85.29 %

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