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Basic information

Entry
Database: PDB / ID: 1c9z
TitleD232-CGTACG
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / INTERCALATOR / INTERCALATION / DRUG / MAJOR GROOVE
Function / homologyChem-232 / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsWilliams, L.D.
CitationJournal: Curr.Med.Chem. / Year: 2000
Title: Effects of cationic charge on three-dimensional structures of intercalative complexes: structure of a bis-intercalated DNA complex solved by MAD phasing.
Authors: Shui, X. / Peek, M.E. / Lipscomb, L.A. / Gao, Q. / Ogata, C. / Roques, B.P. / Garbay-Jaureguiberry, C. / Wilkinson, A.P. / Williams, L.D.
History
DepositionAug 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 17, 2024Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5702
Polymers1,8091
Non-polymers7611
Water00
1
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1404
Polymers3,6182
Non-polymers1,5222
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+3/21
Unit cell
Length a, b, c (Å)28.240, 28.240, 72.744
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-7-

232

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC
#2: Chemical ChemComp-232 / 1,3-DI[[[10-METHOXY-7H-PYRIDO[4,3-C]CARBAZOL-2-IUMYL]-ETHYL]-PIPERIDIN-4-YL]-PROPANE / BIS INTERCALATOR D232


Mass: 761.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H56N6O2

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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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE11
2MGCL211
3SODIUM CACODYLATE11
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.8 mMDNA single strand1drop
215.8 mMsodium cacodylate1drop
32.6 %MPD1drop
40.51 mMspermine1drop
50.66 mM1dropMgCl2
60.37 mMD2321drop
720 %MPD1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Sep 9, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / Num. all: 5220 / Num. obs: 4698 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.2 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / % possible all: 84
Reflection
*PLUS
Num. all: 4698 / Num. obs: 744 / % possible obs: 91 % / Num. measured all: 5220 / Rmerge(I) obs: 0.0514

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Processing

Software
NameVersionClassification
MADSYSphasing
X-PLOR3.851refinement
SDMSdata reduction
SDMSdata scaling
RefinementResolution: 2.4→10 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 99 -RANDOM
Rwork0.1961 ---
obs0.1961 4682 90 %-
all-5220 --
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 29 0 149
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. reflection obs: 731 / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg3.29

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