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- PDB-385d: FORMATION OF A NEW COMPOUND IN THE CRYSTAL STRUCTURE OF CYANOMORP... -

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Basic information

Entry
Database: PDB / ID: 385d
TitleFORMATION OF A NEW COMPOUND IN THE CRYSTAL STRUCTURE OF CYANOMORPHOLINODOXORUBICIN COMPLEXED WITH D(CGATCG)
ComponentsDNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyN-ETHYLHYDROXY-DOXORUBICIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsEttorre, A. / Cirilli, M. / Ughetto, G.
CitationJournal: Eur.J.Biochem. / Year: 1998
Title: Degradation of the morpholino ring in the crystal structure of cyanomorpholinodoxorubicin complexed with d(CGATCG).
Authors: Ettorre, A. / Cirilli, M. / Ughetto, G.
History
DepositionMar 5, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 30, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3972
Polymers1,8091
Non-polymers5881
Water48627
1
A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,7944
Polymers3,6182
Non-polymers1,1752
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)28.130, 28.130, 53.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-NOD / N-ETHYLHYDROXY-DOXORUBICIN


Mass: 587.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33NO12
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE_HCL11
4NA CACODYLATE11
5MGCL211
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mMsodium cacodylate1drop
21.5 mMDNA1drop
39 mM1dropMgCl2
41.5 mMspermine hydrochloride1drop
520 %MPD1drop
61 mMCMD1dropdissolved in methanol
735 %MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Oct 1, 1995
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→8 Å / Num. obs: 3509 / Biso Wilson estimate: 9.18 Å2 / Rmerge(I) obs: 0.121
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 8 Å
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.67 Å / % possible obs: 88.9 %

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Processing

Software
NameClassification
NUCLSQrefinement
TEXSANdata reduction
TEXRAYdata reduction
RefinementResolution: 1.6→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.217 -10 %RANDOM
all0.206 3509 --
obs0.207 1212 --
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 42 27 189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.008
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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