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- PDB-4u92: Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-m... -

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Basic information

Entry
Database: PDB / ID: 4u92
TitleCrystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad
ComponentsDNA (5'-D(*CP*CP*AP*KP*GP*CP*GP*TP*GP*G)-3')
KeywordsDNA / DNA quadruplex Barium C-tetrad
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsPaukstelis, P.J. / Zhang, D. / Huang, T. / Lukeman, P.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad.
Authors: Zhang, D. / Huang, T. / Lukeman, P.S. / Paukstelis, P.J.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _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_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,46010
Polymers5,5882
Non-polymers8738
Water1,09961
1
A: DNA (5'-D(*CP*CP*AP*KP*GP*CP*GP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*KP*GP*CP*GP*TP*GP*G)-3')
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)25,84140
Polymers22,3518
Non-polymers3,49032
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 area10320 Å2
ΔGint-211 kcal/mol
Surface area4860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.621, 29.621, 63.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-101-

BA

21A-102-

BA

31A-103-

BA

41A-105-

MG

51B-101-

BA

61B-102-

BA

71B-103-

BA

81A-214-

HOH

91B-220-

HOH

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Components

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


Mass: 2793.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 3-cyanovinylcarabazole nucleotide at position 4 / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Magnesium chloride hexahydrate, Barium chloride dihydrate, MOPS pH 7.0, 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 8348 / % possible obs: 99.1 % / Redundancy: 14.2 % / Net I/σ(I): 44.25

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.5→26.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.872 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14423 425 4.8 %RANDOM
Rwork0.12931 ---
obs0.13002 8348 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.791 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 254 8 61 323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.011284
X-RAY DIFFRACTIONr_bond_other_d0.0070.02134
X-RAY DIFFRACTIONr_angle_refined_deg1.721.144436
X-RAY DIFFRACTIONr_angle_other_deg1.7393318
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_restr0.1020.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0390.02154
X-RAY DIFFRACTIONr_gen_planes_other0.0080.0264
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_it1.931.462284
X-RAY DIFFRACTIONr_scbond_other1.9331.464283
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7122.165436
X-RAY DIFFRACTIONr_long_range_B_refined4.65415493
X-RAY DIFFRACTIONr_long_range_B_other4.15614.514468
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.134 29 -
Rwork0.121 558 -
obs--93.17 %

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