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- PDB-4mnb: Crystal Structure of a complex between the marine anticancer drug... -

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Basic information

Entry
Database: PDB / ID: 4mnb
TitleCrystal Structure of a complex between the marine anticancer drug Variolin B and DNA
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / DNA duplex / Intercalation / Drug binding / Nucleus
Function / homology: / COBALT HEXAMMINE(III) / Chem-VAR / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCanals, A. / Arribas-Bosacoma, R. / Alvarez, M. / Albericio, F. / Aymami, J. / Coll, M.
CitationJournal: Sci Rep / Year: 2017
Title: Intercalative DNA binding of the marine anticancer drug variolin B.
Authors: Canals, A. / Arribas-Bosacoma, R. / Albericio, F. / Alvarez, M. / Aymami, J. / Coll, M.
History
DepositionSep 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_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_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*TP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7709
Polymers3,6182
Non-polymers1,1527
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-7 kcal/mol
Surface area2810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.700, 53.400, 40.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-104-

CO

21B-101-

NCO

31B-103-

NA

41B-209-

HOH

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Components

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DNA chain , 1 types, 2 molecules AB

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 5 types, 32 molecules

#2: Chemical ChemComp-VAR / 9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol


Mass: 293.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11N7O
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 8% v/v MPD, 40 mM Na Cacodylate pH 5.8, 4 mM Hexamine Cobalt, 12 mM NaCl, 80 mM KCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.4→40.8 Å / Num. all: 6471 / Num. obs: 6465 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.79 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25341 301 4.7 %RANDOM
Rwork0.20813 ---
obs0.21024 6157 99.83 %-
all-6167 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.544 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-0 Å2
2---0.34 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 224 60 25 309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.012311
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg9.4331.513473
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.233
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.02165
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7291.879311
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.84719.79652
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 22 -
Rwork0.313 448 -
obs--100 %

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