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- PDB-3np6: The crystal structure of Berberine bound to DNA d(CGTACG) -

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Basic information

Entry
Database: PDB / ID: 3np6
TitleThe crystal structure of Berberine bound to DNA d(CGTACG)
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / DRUG-DNA COMPLEX / DOUBLE HELIX / B-DNA
Function / homologyBERBERINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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
DepositionJun 28, 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_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: 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)7,6136
Polymers7,2374
Non-polymers3762
Water181
1
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6593
Polymers3,6182
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-2 kcal/mol
Surface area2700 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)3,9553
Polymers3,6182
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-2 kcal/mol
Surface area2700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.370, 30.370, 118.260
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BER / BERBERINE


Mass: 336.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 43.46 %
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: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.542 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jan 22, 2010
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, L10.914
11-h,-k,l20.086
ReflectionResolution: 2.3→39.42 Å / Num. obs: 3159 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.45 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 29.04
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
2.3-2.40.3250.5584.875736546530.58499.8
2.4-2.60.1530.3849.117213101910190.396100
2.6-2.80.0850.2214.8142377387380.226100
2.8-2.90.060.17718.760472912910.181100
2.9-30.0490.13923.957612732730.142100
3-3.120.0380.10429.658912772770.106100
3.12-3.270.020.06541.460922782780.067100
3.27-3.440.0180.05946.158812722720.061100
3.44-3.650.0150.05451.358462632630.056100
3.65-3.940.0170.0652.361522772770.061100
3.94-4.330.0150.05655.260182852850.057100
4.33-4.960.0170.05655.455712592590.058100
4.96-6.250.0150.05756.457762722720.058100
6.25-100.0130.04961.845922112110.05100
10-150.010.04164.686338380.041100
15-39.420.010.036135119190.031100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å39.42 Å
Translation3.5 Å39.42 Å

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Processing

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

1xcs


Resolution: 2.3→39.42 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.2752 / WRfactor Rwork: 0.2204 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7005 / SU ML: 0.212 / SU R Cruickshank DPI: 0.0769 / SU Rfree: 0.0594 / Cross valid method: THROUGHOUT / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3014 139 4.4 %RANDOM
Rwork0.2361 ---
obs0.2387 3153 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 36.44 Å2 / Biso mean: 18.1113 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 450 26 1 477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021531
X-RAY DIFFRACTIONr_angle_refined_deg1.8423813
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A'*3)0.0910.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02258
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A'*2)0.1891.53
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A'*2)0.35824
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A'*2)1.4543528
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A'*2)2.5474.5809
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 6 -
Rwork0.441 212 -
all-218 -
obs--99.54 %

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