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- PDB-360d: STRUCTURE OF 2,5-BIS{[4-(N-ETHYLAMIDINO)PHENYL]}FURAN COMPLEXED T... -

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Basic information

Entry
Database: PDB / ID: 360d
TitleSTRUCTURE OF 2,5-BIS{[4-(N-ETHYLAMIDINO)PHENYL]}FURAN COMPLEXED TO 5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'. A MINOR GROOVE DRUG COMPLEX, SHOWING PATTERNS OF GROOVE HYDRATION
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyChem-BPF / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGuerri, A. / Simpson, I.J. / Neidle, S.
CitationJournal: Nucleic Acids Res. / Year: 1998
Title: Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex.
Authors: Guerri, A. / Simpson, I.J. / Neidle, S.
History
DepositionOct 29, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 16, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 25, 2012Group: Non-polymer description
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Apr 8, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7144
Polymers7,3272
Non-polymers3872
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.240, 39.940, 65.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (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 / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BPF / N,N'-(furan-2,5-diylbis{benzene-4,1-diyl[(Z)-aminomethylylidene]})diethanaminium / DB185 / FURAMIDINE DERIVATIVE


Mass: 362.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 43.48 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 288.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2SODIUM CACODYLATE11
3SPERMINE11
4MGCL211
5MPD11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
23 mMdodecanucleotide1drop
310 mMspermine1drop
43 mMdrug1drop
575 mM1dropMgCl2
625 %(v/w)MPD1drop
730 %(v/w)1reservoir
1sodium cacodylate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→7 Å / Num. obs: 5634 / % possible obs: 91.44 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.022 / Net I/σ(I): 33.18
Reflection shellResolution: 1.854→1.9 Å / Mean I/σ(I) obs: 14.67 / % possible all: 80.7
Reflection
*PLUS
% possible obs: 96.2 % / Num. measured all: 36613 / Rmerge(I) obs: 0.034

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY GDL045 (PDB: 289D)

289d


Resolution: 1.85→7 Å / Num. parameters: 2904 / Num. restraintsaints: 3734 / Cross valid method: NONE / σ(F): 4
StereochEM target val spec case: STEREOCHEMISTRY OF LIGAND FROM MM CALCULATIONS
Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflection
Rwork0.166 --
all-5634 -
obs-5386 91.4 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 260 / Occupancy sum non hydrogen: 733
Refinement stepCycle: LAST / Resolution: 1.85→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 28 219 733
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 7 Å / σ(F): 4 / Rfactor obs: 0.169 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg0.023

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