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- PDB-1z8v: The Structure of d(GGCCAATTGG) Complexed with Netropsin -

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Basic information

Entry
Database: PDB / ID: 1z8v
TitleThe Structure of d(GGCCAATTGG) Complexed with Netropsin
Components(5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
KeywordsDNA / B-DNA DOUBLE HELIX / BASE TRIPLETS / MINOR GROOVE BINDER / DRUG / NETROPSIN
Function / homologyNETROPSIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVan Hecke, K. / Nam, P.C. / Nguyen, M.T. / Van Meervelt, L.
CitationJournal: Febs J. / Year: 2005
Title: Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations.
Authors: Van Hecke, K. / Nam, P.C. / Nguyen, M.T. / Van Meervelt, L.
History
DepositionMar 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 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: (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
B: (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6013
Polymers6,1702
Non-polymers4301
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.025, 38.559, 53.203
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 (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
Details: The oligonucleotide was purchased from Oswel DNA service (University of Southampton, UK)
#2: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic, antivirus*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: potassium cacodylate, MPD, magnesium chloride, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1potassium cacodylate11
2MPD11
3magnesium chloride11
4spermine11
5MPD12
6magnesium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8457 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8457 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 5724 / % possible obs: 98.1 % / Redundancy: 10.7 % / Biso Wilson estimate: 24.74 Å2 / Rsym value: 0.04 / Net I/σ(I): 20.1
Reflection shellResolution: 1.75→1.81 Å / Num. unique all: 538 / Rsym value: 0.199 / % possible all: 96.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY DD0002

Resolution: 1.75→9.6 Å / Isotropic thermal model: isotropic /
RfactorNum. reflection
Rwork0.1997 -
all0.2 -
obs-5379
Displacement parametersBiso mean: 35.7 Å2
Refinement stepCycle: LAST / Resolution: 1.75→9.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 410 31 68 509

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