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- PDB-3nx5: The crystal structure of Sanguinarine bound to DNA d(CGTACG) -

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Basic information

Entry
Database: PDB / ID: 3nx5
TitleThe crystal structure of Sanguinarine bound to DNA d(CGTACG)
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / DRUG-DNA COMPLEX / DOUBLE HELIX
Function / homologyChem-SAU / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsFerraroni, M. / Bazzicalupi, C. / Gratteri, P. / Bilia, A.R.
CitationJournal: Chem.Commun.(Camb.) / Year: 2011
Title: X-Ray diffraction analyses of the natural isoquinoline alkaloids Berberine and Sanguinarine complexed with double helix DNA d(CGTACG)
Authors: Ferraroni, M. / Bazzicalupi, C. / Bilia, A.R. / Gratteri, P.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_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: 5'-D(*CP*GP*TP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
C: 5'-D(*CP*GP*TP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6096
Polymers7,2374
Non-polymers3722
Water905
1
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
B: 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 area360 Å2
ΔGint-3 kcal/mol
Surface area2680 Å2
MethodPISA
2
C: 5'-D(*CP*GP*TP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9914
Polymers3,6182
Non-polymers3722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-2 kcal/mol
Surface area2680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.992, 29.992, 119.069
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
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-SAU / 13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium / Sanguinarine


Mass: 332.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14NO4
#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.: 5 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5
Details: MPD, MgCl2, NaCl, pH 6.5, vapor diffusion, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2010
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.746
11h+k,-k,-l20.254
ReflectionResolution: 2.29→39.69 Å / Num. obs: 3006 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 47.698 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 20.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.29-2.430.1250.1126.511394704000.13385.1
2.43-2.60.0690.09413.824974734730.105100
2.6-2.810.0440.07619.523514164150.08499.8
2.81-3.070.0370.06423.321713993990.071100
3.07-3.430.0250.04527.119573683650.0599.2
3.43-3.960.0310.05328.717523313300.05999.7
3.96-4.840.0280.04828.514362802800.054100
4.84-6.790.0270.04927.610932382320.05597.5
6.79-39.690.0220.0425.24511481120.04675.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å39.69 Å
Translation3.5 Å39.69 Å

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Processing

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

3np6


Resolution: 2.31→39.69 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.3248 / WRfactor Rwork: 0.2852 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5756 / SU B: 14.156 / SU ML: 0.294 / SU R Cruickshank DPI: 0.0981 / SU Rfree: 0.0596 / Cross valid method: THROUGHOUT / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2833 289 9.6 %RANDOM
Rwork0.2521 ---
obs0.2552 2719 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.94 Å2 / Biso mean: 33.9258 Å2 / Biso min: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1--22.27 Å20 Å20 Å2
2---22.27 Å20 Å2
3---44.54 Å2
Refinement stepCycle: LAST / Resolution: 2.31→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 450 26 5 481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021532
X-RAY DIFFRACTIONr_angle_refined_deg2.4033816
X-RAY DIFFRACTIONr_chiral_restr0.0630.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02257
X-RAY DIFFRACTIONr_mcbond_it0.4951.53
X-RAY DIFFRACTIONr_mcangle_it1.12923
X-RAY DIFFRACTIONr_scbond_it1.4693529
X-RAY DIFFRACTIONr_scangle_it2.3874.5813
LS refinement shellResolution: 2.305→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.974 24 -
Rwork0.79 168 -
all-192 -
obs--87.67 %

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