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- PDB-261d: CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 261d
TitleCRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / FLIPPED-OUT BASES / INTERMOLECULAR BASE TRIPLET / CONTINUOUS HELIX / COMPLEXED WITH DRUG
Function / homologyNETROPSIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsNunn, C.M. / Garman, E. / Neidle, S.
CitationJournal: Biochemistry / Year: 1997
Title: Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin.
Authors: Nunn, C.M. / Garman, E. / Neidle, S.
History
DepositionNov 8, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 22, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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: DNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5203
Polymers6,0902
Non-polymers4301
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.840, 39.800, 54.080
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 DNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NT / NETROPSIN


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


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4WATER12
5MPD12
6NA CACODYLATE12
Crystal grow
*PLUS
Temperature: 291 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.83 mMDNA1drop
21.7 mMnetropsin1drop
30.17 M1dropMgCl2
411 %MPD1drop
545 %1reservoir
61

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 12, 1994
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. all: 4063 / Num. obs: 1864 / % possible obs: 82 % / Rmerge(I) obs: 0.03
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 82 %

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Processing

Software
NameClassification
XDSdata scaling
X-PLORrefinement
XDSdata reduction
RefinementResolution: 2.4→8 Å / σ(F): 2
Details: NUCLEIC ACID RNA-DNA PARAMETER FILE: G. PARKINSON ET AL. (1996) ACTA CRYST. D52, 57-64
RfactorNum. reflection
Rwork0.201 -
obs0.201 1773
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 385 31 85 501
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: NDB_PARAMETER_FILE.DNA / Topol file: NDB_TOPOLOGY_FILE.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.8

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