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- PDB-1qv8: B-DNA Dodecamer d(CGCGAATTCGCG)2 complexed with proamine -

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Basic information

Entry
Database: PDB / ID: 1qv8
TitleB-DNA Dodecamer d(CGCGAATTCGCG)2 complexed with proamine
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / B-DNA / minor groove binder
Function / homologyChem-BBZ / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSquire, C.J. / Clark, G.R.
CitationJournal: Cancer Res. / Year: 2004
Title: In vitro studies with methylproamine: a potent new radioprotector.
Authors: Martin, R.F. / Broadhurst, S. / Reum, M.E. / Squire, C.J. / Clark, G.R. / Lobachevsky, P.N. / White, J.M. / Clark, C. / Sy, D. / Spotheim-Maurizot, M. / Kelly, D.P.
History
DepositionAug 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Feb 14, 2024Group: 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

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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)7,7783
Polymers7,3272
Non-polymers4521
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.310, 40.400, 65.920
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(*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
#2: Chemical ChemComp-BBZ / 2'-(4-DIMETHYLAMINOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE


Mass: 451.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29N7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MgCl2, cacodylate, MPD, spermine HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2cacodylate11
3MPD11
4spermine11
5HCl11
6H2O11
7MgCl212
8cacodylate12
9MPD12
10spermine12
11H2O12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 0.71073 Å
DetectorType: SIEMENS / Detector: CCD / Date: Jul 26, 1997
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71073 Å / Relative weight: 1
ReflectionResolution: 2.5→500 Å / Num. obs: 2611 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.59 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SiemensSMARTdata collection
SAINT& SADABSdata reduction
CNSrefinement
SMART(SIEMENS)data reduction
SAINTdata scaling
SADABSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.269 220 8.9 %
Rwork0.219 --
all0.21 --
obs0.21 2348 94.8 %
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 34 17 537
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d1.9
X-RAY DIFFRACTIONc_angle_deg3.4
X-RAY DIFFRACTIONc_mcbond_it1.9171.5
X-RAY DIFFRACTIONc_scbond_it2.0982
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it3.3572.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_rep.param
X-RAY DIFFRACTION2pro.param
X-RAY DIFFRACTION3water_rep.param

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