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- PDB-4d9x: The crystal structure of Coptisine bound to DNA d(CGTACG) -

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Basic information

Entry
Database: PDB / ID: 4d9x
TitleThe crystal structure of Coptisine bound to DNA d(CGTACG)
ComponentsDNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / DRUG-DNA COMPLEX / DOUBLE HELIX
Function / homologyChem-KPT / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.44 Å
AuthorsFerraroni, M. / Bazzicalupi, C. / Gratteri, P. / Bilia, A.R.
CitationJournal: to be published
Title: The crystal structure of Coptisine 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 1.1Sep 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)7,5976
Polymers7,2374
Non-polymers3602
Water27015
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)3,6593
Polymers3,6182
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-3 kcal/mol
Surface area2700 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9393
Polymers3,6182
Non-polymers3201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-8 kcal/mol
Surface area2720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.282, 30.282, 118.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6
Details: MPD, MgCl2, KCl, spermine, pH 6.0, VAPOR DIFFUSION, 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 / Detector: CCD / Date: Aug 9, 2010 / Details: OXFORD ONYX CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.789
11h+k,-k,-l20.211
ReflectionResolution: 2.44→30 Å / Num. obs: 2642 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.967 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 17.48
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.44-2.590.6114.015437404197.3
2.59-2.770.3527.258293981100
2.77-2.990.2569.7850673511100
2.99-3.270.12318.2947323281100
3.27-3.640.09225.4342583061100
3.64-4.190.08528.2137482811100
4.19-5.110.07728.3532772451100
5.11-7.090.07229.524591931100
7.09-300.06728.821462136199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å26.23 Å
Translation3.5 Å26.23 Å

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Processing

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

3np6


Resolution: 2.44→30 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.3123 / WRfactor Rwork: 0.2595 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7534 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1476 / SU Rfree: 0.0734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Used twin refinement twin fraction 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.3074 254 9.6 %RANDOM
Rwork0.2614 ---
obs0.2659 2641 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.38 Å2 / Biso mean: 24.6741 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 2.44→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 450 25 15 490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021531
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9553814
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_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02258
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.734 15 -
Rwork0.488 175 -
all-190 -
obs--94.06 %

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