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- PDB-5hix: Cocrystal structure of an anti-parallel DNA G-quadruplex and a te... -

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Basic information

Entry
Database: PDB / ID: 5hix
TitleCocrystal structure of an anti-parallel DNA G-quadruplex and a tetra-Quinoline Foldamer
ComponentsDimeric G-quadruplex
KeywordsDNA / DNA G-quadruplex / Foldamer / Foldamer-quadruplex / G-quadruplex Ligands
Function / homologyChem-61Q / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsMandal, P.K. / Baptiste, B. / Langlois d'Estaintot, B. / Kauffmann, B. / Huc, I.
Funding support France, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-320892 France
CitationJournal: Chembiochem / Year: 2016
Title: Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State.
Authors: Mandal, P.K. / Baptiste, B. / Langlois d'Estaintot, B. / Kauffmann, B. / Huc, I.
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dimeric G-quadruplex
B: Dimeric G-quadruplex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7887
Polymers7,6112
Non-polymers1,1775
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-18 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.701, 31.701, 97.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: DNA chain Dimeric G-quadruplex


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Oxytricha Nova / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-61Q / 4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-nitroquinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinoline-2-carboxylic acid


Mass: 1021.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C52H52N12O11
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: d(GGGGTTTTGGGG), 8-amino-2-quinolinecarboxylic acid, potassium cacodylate, magnesium chloride, potassium chloride, spermine, 2-methyl-2,4-pentanediol (MPD)
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.519
11-H, K, -L20.481
ReflectionResolution: 2.48→30.14 Å / Num. obs: 3345 / % possible obs: 97.72 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.06
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.95 / % possible all: 88.62

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JRN

1jrn


Resolution: 2.48→30.14 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.537 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28784 157 4.7 %RANDOM
Rwork0.22694 ---
obs0.23052 3151 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.927 Å2
Baniso -1Baniso -2Baniso -3
1-31.99 Å20 Å20 Å2
2--31.99 Å20 Å2
3----63.98 Å2
Refinement stepCycle: 1 / Resolution: 2.48→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 79 10 595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.012650
X-RAY DIFFRACTIONr_bond_other_d0.0150.021329
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.341994
X-RAY DIFFRACTIONr_angle_other_deg3.563.065772
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_restr0.0840.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021375
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02127
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_it6.4675.759650
X-RAY DIFFRACTIONr_scbond_other6.4635.768651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2968.601995
X-RAY DIFFRACTIONr_long_range_B_refined12.65162.0441225
X-RAY DIFFRACTIONr_long_range_B_other12.64762.1051225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.481→2.545 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.516 6 -
Rwork0.309 192 -
obs--78.57 %

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