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- PDB-482d: RELEASE OF THE CYANO MOIETY IN THE CRYSTAL STRUCTURE OF N-CYANOME... -

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Basic information

Entry
Database: PDB / ID: 482d
TitleRELEASE OF THE CYANO MOIETY IN THE CRYSTAL STRUCTURE OF N-CYANOMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN COMPLEXED WITH D(CGATCG)
Components5'-D(*CP*GP*AP*TP*CP*G)-3'
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / DEOXYRIBONUCLEIC ACID
Function / homologyN-HYDROXYMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsSaminadin, P. / Dautant, A. / Mondon, M. / Langlois D'Estaintot, B. / Courseille, C. / Precigoux, G.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: Release of the cyano moiety in the crystal structure of N-cyanomethyl-N-(2-methoxyethyl)-daunomycin complexed with d(CGATCG).
Authors: Saminadin, P. / Dautant, A. / Mondon, M. / Langlois D'estaintot, B. / Courseille, C. / Precigoux, G.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: Degradation of the Morpholino Ring in the Crystal Structure of Cyanomorpholinodoxorubicin
Authors: Ettorre, A. / Cirilli, M. / Ughetto, G.
#2: Journal: Biochemistry / Year: 1990
Title: Structural Comparison of Anticancer Drug-DNA Complexes. Adriamycin and Daunomycin
Authors: Frederick, C.A. / Williams, L.D. / Ughetto, G. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.-J.
History
DepositionJul 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4272
Polymers1,8091
Non-polymers6181
Water45025
1
A: 5'-D(*CP*GP*AP*TP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,8544
Polymers3,6182
Non-polymers1,2352
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)28.160, 28.160, 53.400
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 5'-D(*CP*GP*AP*TP*CP*G)-3'


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: COMPLEXED WITH (2-METHOXYETHYL)-DAUNOMYCIN
#2: Chemical ChemComp-DM9 / N-HYDROXYMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN


Mass: 617.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39NO12
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-CYANOMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN WAS USED IN CRYSTALLIZATION SET-UP. DEGRADATION OF THIS ...N-CYANOMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN WAS USED IN CRYSTALLIZATION SET-UP. DEGRADATION OF THIS COMPOUND GAVE RISE TO N-HYDROXYMETHYL-N(-2-METHOXYETHYL)-DAUNOMYCIN.

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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: 2.24 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED MPD, LICL, MGCL2, SODIUM CACODYLATE, COBALT HEXAMINE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2LICL11
3MGCL211
4SODIUM CACODYLATE11
5[CO(NH3)6]CL311
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.2 mMd(CGATCG)1drop
23.3 mMdrug1drop
323 %dimethylsulfoxide1drop
473 mMsodium cacodylate1drop
540 mM1dropLiCl
620 mM1dropMgCl2
720 mMcobalt hexamine1drop
810 %(v/v)MPD1drop
935 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→12.6 Å / Num. obs: 3327 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 9.6
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.158 / % possible all: 92.3
Reflection shell
*PLUS
% possible obs: 92.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEE REMARK 1 REFERENCE 2

Resolution: 1.54→12.6 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 136 10 %RANDOM
Rwork0.23 ---
obs0.23 3220 92 %-
Displacement parametersBiso mean: 19.9 Å2
Refinement stepCycle: LAST / Resolution: 1.54→12.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 44 25 189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.386
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d0.601
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.996
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.43 6 10 %
Rwork0.23 181 -
obs--84 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg0.601
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.996

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