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- PDB-1qda: Crystal structure of epidoxorubicin-formaldehyde virtual crosslin... -

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Basic information

Entry
Database: PDB / ID: 1qda
TitleCrystal structure of epidoxorubicin-formaldehyde virtual crosslink of DNA
Components5' -D(CP*GP*CP*(G49)P*CP*GP)-3'
KeywordsDNA / DOUBLE HELIX / DRUG-DNA COMPLEX
Function / homology4'-EPIDOXORUBICIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsPodell, E.R. / Harrington, D.J. / Taatjes, D.J. / Koch, T.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystal structure of epidoxorubicin-formaldehyde virtual crosslink of DNA and evidence for its formation in human breast-cancer cells.
Authors: Podell, E.R. / Harrington, D.J. / Taatjes, D.J. / Koch, T.H.
#1: Journal: Curr.Pharm.Des. / Year: 1998
Title: A redox pathway leading to the alkylation of nucleic acids by doxorubicin and related anthracyclines: application to the design of antitumor drugs for resistant cancer.
Authors: Taatjes, D.J. / Fenick, D.J. / Gaudiano, G. / Koch, T.H.
#2: Journal: J.Med.Chem. / Year: 1998
Title: Epidoxoform: A Hydrolytically More Stable Anthracycline-Formaldehyde Conjugate Toxic to Resistant Tumor Cells
Authors: Taatjes, D.J. / Fenick, D.J. / Koch, T.H.
History
DepositionMay 17, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 12, 2014Group: Database references
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 5' -D(CP*GP*CP*(G49)P*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3692
Polymers1,8241
Non-polymers5451
Water54030
1
A: 5' -D(CP*GP*CP*(G49)P*CP*GP)-3'
hetero molecules

A: 5' -D(CP*GP*CP*(G49)P*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7384
Polymers3,6482
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)28.110, 28.110, 52.540
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*CP*(G49)P*CP*GP)-3'


Mass: 1824.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DOXORUBICIN COVALENTLY ATTACHED TO N2(G4) VIA METHYLENE BRIDGE
#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.: 30 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, FORMALDEHYDE, CACODYLATE, SPERMINE, BARIUM CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1FORMALDEHYDE11
2SODIUM CACODYLATE11
3SPERMINE11
4BACL211
5MPD11
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mMd(CGCGCG)1drop
21.2 mMepidoxorubicin1drop
39 mMformaldehyde1drop
430 mMsodium cacodylate1drop
516.1 mMspermine1drop
64.4 mM1dropBaCl2
740 %MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 3101 / Num. obs: 3101 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.309 / % possible all: 82.7
Reflection
*PLUS
Num. measured all: 47174
Reflection shell
*PLUS
% possible obs: 82.7 % / Num. unique obs: 2482

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN
Details: USED ALL THE REFLECTIONS IN THE FINAL SERIES OF REFINEMENT CYCLES
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 529 17.3 %RANDOM
Rwork0.2052 ---
obs0.2052 2612 84.5 %-
all-3091 --
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 121 39 30 190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 17.3 % / Rfactor all: 0.2164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.37 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.1

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