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- PDB-258d: FACTORS AFFECTING SEQUENCE SELECTIVITY ON NOGALAMYCIN INTERCALATI... -

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Basic information

Entry
Database: PDB / ID: 258d
TitleFACTORS AFFECTING SEQUENCE SELECTIVITY ON NOGALAMYCIN INTERCALATION: THE CRYSTAL STRUCTURE OF D(TGTACA)-NOGALAMYCIN
ComponentsDNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyACETATE ION / NOGALAMYCIN / SPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsSmith, C.K. / Brannigan, J.A. / Moore, M.H.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Factors affecting DNA sequence selectivity of nogalamycin intercalation: the crystal structure of d(TGTACA)2-nogalamycin2.
Authors: Smith, C.K. / Brannigan, J.A. / 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.
#2: 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.
History
DepositionMay 12, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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*TP*AP*CP*A)-3')
B: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
C: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
D: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,72812
Polymers7,2334
Non-polymers3,4958
Water1,74797
1
A: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
B: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5358
Polymers3,6162
Non-polymers1,9196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
D: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1924
Polymers3,6162
Non-polymers1,5762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.300, 51.980, 67.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 1 types, 4 molecules ABCD

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


Mass: 1808.229 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Non-polymers , 5 types, 105 molecules

#2: Chemical
ChemComp-NGM / NOGALAMYCIN / Nogalamycin


Mass: 787.803 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H49NO16 / Comment: antitumor, antibiotic*YM
#3: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4NA CACODYLATE11
5MG ACETATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.3 mMdouble-stranded oligonucleotide1drop
21.6 mMnogalamycin1drop
320 mMsodium cacodylate1drop
418 mMmagnesium acetate1drop
58-10 %(v/v)MPD1drop
60.4 mMspermine1drop
71reservoir0.100ml

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31
DetectorType: HENDRIX-LENTFER / Detector: IMAGE PLATE / Date: Jul 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.58→10.69 Å / Num. obs: 13148 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.58→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.196 / % possible all: 69.5
Reflection
*PLUS
Highest resolution: 1.58 Å / Lowest resolution: 10.69 Å

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Processing

Software
NameClassification
AMoREphasing
SHELXL-93refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY DDF049 (PDB: 182D)

182d


Resolution: 1.58→10.69 Å / Num. parameters: 3310 / Num. restraintsaints: 12049 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: TAYLOR AND KENNARD / Details: ESTIMATED COORDINATE ERROR (A) : 0.12A
RfactorNum. reflection% reflection
Rfree0.237 1235 10 %
Rwork0.188 --
all0.192 12358 -
obs0.188 12358 94 %
Solvent computationSolvent model: BABINET'S PRINCIPLE
Displacement parametersBiso mean: 21.78 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.58→10.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 247 97 824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist0.023
X-RAY DIFFRACTIONs_from_restr_planes0.089
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.022
X-RAY DIFFRACTIONs_approx_iso_adps0.057
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.58 Å / Lowest resolution: 10.69 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.089

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