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- PDB-1d58: THE MOLECULAR STRUCTURE OF A 4'-EPIADRIAMYCIN COMPLEX WITH D(TGAT... -

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Basic information

Entry
Database: PDB / ID: 1d58
TitleTHE MOLECULAR STRUCTURE OF A 4'-EPIADRIAMYCIN COMPLEX WITH D(TGATCA) AT 1.7 ANGSTROM RESOLUTION-COMPARISON WITH THE STRUCTURE OF 4'-EPIADRIAMYCIN D(TGTACA) AND D(CGATCG) COMPLEXES
ComponentsDNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homology4'-EPIDOXORUBICIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsLanglois D'Estaintot, B. / Gallois, B. / Brown, T. / Hunter, W.N.
CitationJournal: Nucleic Acids Res. / Year: 1992
Title: The molecular structure of a 4'-epiadriamycin complex with d(TGATCA) at 1.7A resolution: comparison with the structure of 4'-epiadriamycin d(TGTACA) and d(CGATCG) complexes.
Authors: Langlois d'Estaintot, B. / Gallois, B. / Brown, T. / Hunter, W.N.
History
DepositionFeb 20, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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: DNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3532
Polymers1,8081
Non-polymers5451
Water61334
1
A: DNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
hetero molecules

A: DNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7064
Polymers3,6162
Non-polymers1,0892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)28.014, 28.014, 52.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM6 / 4'-EPIDOXORUBICIN / 4'-EPIADRIAMYCIN


Mass: 544.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30NO11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MG ACETATE11
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMDNA1drop
21.2 mM4'-epiadriamycin1drop
3100 mMsodium cacodylate1drop
4140 mMmagnesium acetate1drop
50.5 mMspermine hydrochloride1drop
611 % v/v2-methyl-2,4-pentanediol1drop
780 % v/v2-methyl-2,4-pentanediol1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. all: 10067 / Num. obs: 5730
Reflection
*PLUS
Highest resolution: 1.7 Å / Rmerge(I) obs: 0.102

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.7→7 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.202 -
obs0.202 1694
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL DRUGSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 39 34 193
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 7 Å / σ(F): 2 / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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