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- PDB-1jux: 1.6A Resolution Crystal Structures of the DNA Octamers d(IUATATAC... -

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Basic information

Entry
Database: PDB / ID: 1jux
Title1.6A Resolution Crystal Structures of the DNA Octamers d(IUATATAC) and d(ITITACAC):Binding of Two Distamycin Drugs Side-by-Side
Components5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'
KeywordsDNA / Octamer / Distamycin / Side-by-Side
Function / homologyDISTAMYCIN A / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDeng, J. / Pan, B. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of d(ITITACAC) complexed with distamycin at 1.6 A resolution.
Authors: Deng, J. / Pan, B. / Sundaralingam, M.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,8782
Polymers2,3971
Non-polymers4821
Water64936
1
A: 5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'
hetero molecules

A: 5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7564
Polymers4,7932
Non-polymers9632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)33.260, 25.050, 28.300
Angle α, β, γ (deg.)90.00, 124.23, 90.00
Int Tables number5
Space group name H-MC121
DetailsOne strand in the assymetric unit. The duplex is generated by the 2 fold axis.

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Components

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


Mass: 2396.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Octamer DNA
#2: Chemical ChemComp-DMY / DISTAMYCIN A / DISTAMYCIN / STALLIMYCIN / Distamycin


Mass: 481.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N9O4 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.96 Å3/Da / Density % sol: 37.09 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMDNA1dropsingle-stranded concentration
230 mMsodium cacodylate1droppH7.0
30.1 mMcobalt hexammine chloride1drop
41 mMdistamycin hydrochloride1drop
560 %MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 20, 1997
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→10 Å / Num. all: 2609 / Num. obs: 2468 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Num. obs: 2737 / % possible obs: 92 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / % possible obs: 88.8 % / Num. unique obs: 381 / Rmerge(I) obs: 0.162

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.179 234 -random
Rwork0.149 ---
all-2609 --
obs-2468 94.6 %-
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 159 35 36 230
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 2520 / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.006
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.3

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