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- PDB-3oie: Crystal structure of the DB1880-D(CGCGAATTCGCG)2 complex -

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Basic information

Entry
Database: PDB / ID: 3oie
TitleCrystal structure of the DB1880-D(CGCGAATTCGCG)2 complex
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / NUCLEIC ACIDS / DOUBLE HELIX / MINOR GROOVE / DNA MINOR GROOVE BINDER / DNA MINOR GROOVE-LIGAND COMPLEX / DB1880 / A2T2 / DICKERSON AND DREW DODECAMER / CRYSTAL STRUCTURE OF B-DNA / DNA-DRUG COMPLEX / MAGNESIUM-WATER COMPLEX / HYDRATED MAGNESIUM / DNA HYDRATION
Function / homologyChem-881 / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLin, S. / Neidle, S. / Campbell, N.
CitationJournal: To be Published
Title: Crystal structure of the DB1880-D(CGCGAATTCGCG)2 complex
Authors: Lin, S. / Neidle, S. / Campbell, N.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0084
Polymers7,3272
Non-polymers6812
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-9 kcal/mol
Surface area4450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.114, 38.417, 66.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: A2T2 Duplex
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-881 / N',N''-{furan-2,5-diylbis[3-(piperidin-4-yloxy)benzene-4,1-diyl]}dipyridine-2-carboximidamide / DB1880


Mass: 656.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H40N8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MAGNESIUM CHLORIDE, DNA, COMPOUND, DB1880, MPD, SODIUM CACODYLATE BUFFER, pH 6.5, vapor diffusion, hanging drop, temperature 283K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: CCD / Detector: CCD / Date: Mar 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→33.228 Å / Num. all: 5003 / Num. obs: 5003 / % possible obs: 96.2 % / Redundancy: 3.4 % / Rsym value: 0.036 / Net I/σ(I): 20.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-22.10.13512285870.1380.4
2-2.1230.1116.920166710.11197.5
2.12-2.273.70.0938.124546580.09399.2
2.27-2.453.80.06810.922936110.06899.3
2.45-2.693.80.0471521785780.04799.7
2.69-33.70.03917.619485220.03999.9
3-3.473.70.0364.717364710.03699.9
3.47-4.253.60.02613.814384030.026100
4.25-6.013.60.02127.411603220.02199.2
6.01-22.6583.30.02715.75911800.02792.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CrysalisProdata collection
CrysalisProdata reduction
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→22.66 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.233 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 229 4.6 %RANDOM
Rwork0.163 ---
obs0.1667 4962 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.95 Å2 / Biso mean: 21.783 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 50 136 672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021599
X-RAY DIFFRACTIONr_angle_refined_deg3.0313.011911
X-RAY DIFFRACTIONr_chiral_restr0.1250.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02301
X-RAY DIFFRACTIONr_scbond_it2.5053599
X-RAY DIFFRACTIONr_scangle_it3.2944.5911
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 15 -
Rwork0.192 261 -
all-276 -
obs--74.59 %

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