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- PDB-3tvb: A Highly Symmetric DNA G-4 Quadruplex/drug Complex -

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Basic information

Entry
Database: PDB / ID: 3tvb
TitleA Highly Symmetric DNA G-4 Quadruplex/drug Complex
ComponentsDNA (5'-D(*GP*GP*GP*G)-3')
KeywordsDNA/antibiotic / G-4 Quadruplex / Daunomycin / DNA-Drug Complex / DNA-antibiotic complex
Function / homologyDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.08 Å
AuthorsClark, G.R. / Pytel, P.D. / Squire, C.J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages.
Authors: Clark, G.R. / Pytel, P.D. / Squire, C.J.
History
DepositionSep 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Jan 29, 2020Group: Advisory / Data collection / Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_biol / struct_conn / struct_conn_type
Revision 1.3Feb 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*G)-3')
B: DNA (5'-D(*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,88616
Polymers2,5442
Non-polymers2,34314
Water1,982110
1
A: DNA (5'-D(*GP*GP*GP*G)-3')
B: DNA (5'-D(*GP*GP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*GP*G)-3')
B: DNA (5'-D(*GP*GP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*GP*G)-3')
B: DNA (5'-D(*GP*GP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*GP*G)-3')
B: DNA (5'-D(*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,54564
Polymers10,1758
Non-polymers9,37056
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area9450 Å2
ΔGint-265 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.209, 40.209, 49.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-13-

NA

21A-14-

NA

31A-15-

NA

41B-16-

NA

51B-17-

NA

61B-18-

NA

71B-19-

NA

81B-20-

NA

91B-21-

MG

101B-22-

MG

111A-101-

HOH

121A-103-

HOH

131B-106-

HOH

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Components

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


Mass: 1271.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic oligomer
#2: Chemical
ChemComp-DM1 / DAUNOMYCIN / DAUNORUBICIN


Mass: 527.520 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H29NO10
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.96 Å3/Da / Density % sol: 68.93 %
Crystal growTemperature: 277 K / Method: sitting drop / pH: 7
Details: NATRIX NR46 droplets 0.005 M Magnesium sulfate, 0.05 M Tris HCl buffer at pH 8.5, 35% w/v 1,6-hexane diol, Sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.006 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 1.08→10 Å / Num. all: 21428 / Num. obs: 21428 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Redundancy: 66.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 81.79
Reflection shellResolution: 1.08→1.13 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 15.14 / % possible all: 99.2

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: NONE

Resolution: 1.08→10 Å / Num. parameters: 2579 / Num. restraintsaints: 2250 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 1677 11 %RANDOM
Rwork0.1591 ---
all0.164 15269 --
obs0.1618 14501 89.8 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 430.19
Refinement stepCycle: LAST / Resolution: 1.08→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 170 162 110 442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.072
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.019
X-RAY DIFFRACTIONs_approx_iso_adps0

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