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- PDB-224d: DNA-DRUG REFINEMENT: A COMPARISON OF THE PROGRAMS NUCLSQ, PROLSQ,... -

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Basic information

Entry
Database: PDB / ID: 224d
TitleDNA-DRUG REFINEMENT: A COMPARISON OF THE PROGRAMS NUCLSQ, PROLSQ, SHELXL93 AND X-PLOR, USING THE LOW TEMPERATURE D(TGATCA)-NOGALAMYCIN STRUCTURE
ComponentsDNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyNOGALAMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsSchuerman, G.S. / Smith, C.K. / Turkenburg, J.P. / Dettmar, A.N. / Van Meervelt, L. / Moore, M.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: DNA-drug refinement: a comparison of the programs NUCLSQ, PROLSQ, SHELXL93 and X-PLOR, using the low-temperature d(TGATCA)-nogalamycin structure.
Authors: Schuerman, G.S. / Smith, C.K. / Turkenburg, J.P. / Dettmar, A.N. / Van Meervelt, L. / Moore, M.H.
#1: Journal: Biochemistry / Year: 1995
Title: DNA-Nogalamycin Interactions: The Crystal Structure of d(TGATCA) Complexed with Nogalamycin
Authors: Smith, C.K. / Davies, G.J. / Dodson, E.J. / Moore, M.H.
History
DepositionAug 1, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 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 / pdbx_struct_special_symmetry / 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(*TP*GP*AP*TP*CP*A)-3')
B: DNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1924
Polymers3,6162
Non-polymers1,5762
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.290, 37.290, 71.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-90-

HOH

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Components

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


Mass: 1808.229 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NGM / NOGALAMYCIN


Mass: 787.803 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H49NO16
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HMD11
3SPERMINE11
4MGCL211
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 mMoligonucleotide1drop
22.7 mMnogalamycin1drop
35 %1,6-hexanediol1drop
41 mMspermine1drop
517 mM1dropMgCl2
6sodium cacodylate1drop
7100 %1reservoir

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Data collection

DiffractionMean temperature: 150 K
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 9852
Reflection
*PLUS
Highest resolution: 1.4 Å
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.47 Å / Num. unique obs: 1466 / Num. measured obs: 4641 / Rmerge(I) obs: 0.213

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.4→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.274 --
obs0.228 9813 95.6 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 115 77 432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0310.02
X-RAY DIFFRACTIONp_chiral_restr0.1290.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2730.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d

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