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- PDB-245d: DNA-DRUG REFINEMENT: A COMPARISON OF THE PROGRAMS NUCLSQ, PROLSQ,... -

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Basic information

Entry
Database: PDB / ID: 245d
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 / SYNCHROTRON / 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
DepositionJan 12, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 7, 1996Provider: 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 / 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
Water1,18966
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-77-

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 / Comment: antitumor, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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, hanging drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HMD11
3SPERMINE11
4MGCL211
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 mMoligonucleotide1drop
22.7 mMnogalamycin1drop
35 %HMD1drop
41 mMspermine1drop
517 mM1dropMgCl2
6sodium cacodylate1drop
7100 %1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionHighest resolution: 1.4 Å / Num. all: 62880 / Num. obs: 10306 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036
Reflection
*PLUS
Num. obs: 2230 / % possible obs: 97.5 % / Num. measured all: 13447 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 86.8 % / Rmerge(I) obs: 0.21

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Processing

Software
NameClassification
SHELXL-93refinement
DENZOdata reduction
CCP4data reduction
RefinementResolution: 1.4→8 Å / σ(F): 0
Details: DISTANCES AND ANGLES WITHIN THE BASES WERE RESTRAINED TO TARGET VALUES. ALL OTHER CHEMICALLY EQUIVALENT BOND DISTANCES WERE RESTRAINED TO BE SIMILAR BY SAME DISTANCE RESTRAINTS. SIGMAS FOR ...Details: DISTANCES AND ANGLES WITHIN THE BASES WERE RESTRAINED TO TARGET VALUES. ALL OTHER CHEMICALLY EQUIVALENT BOND DISTANCES WERE RESTRAINED TO BE SIMILAR BY SAME DISTANCE RESTRAINTS. SIGMAS FOR BOTH TARGET AND SIMILAR DISTANCE RESTRAINTS WERE SET AT 0.030 ANGSTROMS FOR BONDS AND 0.050 ANGSTROMS FOR ANGLES. SADI_* 0.15 C3'_- P C3'_1 P_2 SADI_* 0.15 C5' P C5'_2 P_2 ISOR 0.1 ISOR 0.05 C2_3 C2_5 ISOR 0.025 C15B_41 DELU C15B_41 O10B_41 C14_41 C10_41 C20_ 41 DELU O5'_21 C5'_21 C4'_21 C3'_21 C2'_21 C1'_21 O4'_21 BUMP
RfactorNum. reflection
Rfree0.252 -
obs0.16 9813
all-9813
Displacement parametersBiso mean: 18.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 115 66 421
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refine LS restraints
*PLUS
Type: s_angle_deg / Dev ideal: 4.22

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