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- PDB-432d: D(GGCCAATTGG) COMPLEXED WITH DAPI -

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Basic information

Entry
Database: PDB / ID: 432d
TitleD(GGCCAATTGG) COMPLEXED WITH DAPI
ComponentsDNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DNA-DRUG COMPLEX / TRIPLET FORMATION / 4' / 6-DIAMIDINO-2-PHENYL INDOLE / DAPI / MINOR GROOVE BINDER
Function / homology6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å
AuthorsVlieghe, D. / Van Meervelt, L.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode.
Authors: Vlieghe, D. / Sponer, J. / Van Meervelt, L.
History
DepositionOct 14, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,4473
Polymers6,1702
Non-polymers2771
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.616, 36.563, 52.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-DAP / 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE


Mass: 277.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3SPERMINE11
4MPD11
5MPD12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
143 mM1dropMgCl2
23 %MPD1drop
32 mMspermine1drop
40.4 mMssDMA1drop
50.2 mMDAPI1drop
650 %MPD1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.89→10 Å / Num. all: 4106 / Num. obs: 4106 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.78
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.55 / % possible all: 95.1
Reflection
*PLUS
Num. obs: 4115 / Num. measured all: 24368
Reflection shell
*PLUS
% possible obs: 95.1 %

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Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: BD0006 USED AS STARTING MODEL FOR REFINEMENT

Resolution: 1.89→10 Å / Num. parameters: 2051 / Num. restraintsaints: 2080 / Cross valid method: NONE
StereochEM target val spec case: DAPI DICTIONARY BASED ON CSD
Stereochemistry target values: TAYLOR AND KENNARD
RfactorNum. reflection% reflection
all0.192 4106 -
obs-3562 97.1 %
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 512
Refinement stepCycle: LAST / Resolution: 1.89→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 410 21 81 512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0.023
X-RAY DIFFRACTIONs_from_restr_planes0.091
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.002
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0

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