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- PDB-3t86: d(GCATGCT) + calcium -

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Basic information

Entry
Database: PDB / ID: 3t86
Titled(GCATGCT) + calcium
ComponentsDNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
KeywordsDNA / quadruplex / loop
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCardin, C.J. / Gan, Y.
CitationJournal: To be Published
Title: A novel structure for the d(GCATGCT) quadruplex in the presence of nickel and cobalt aqueous cations : comparison with the vanadium, barium and calcium-bound structural motif.
Authors: Gan, Y. / Thorpe, J.H. / Teixeira, S.C.M. / Naseer, A. / Cardin, C.J.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
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 / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1933
Polymers2,1131
Non-polymers792
Water18010
1
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,77012
Polymers8,4544
Non-polymers3178
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area2270 Å2
ΔGint-26 kcal/mol
Surface area4700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.742, 58.341, 23.669
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-8-

K

21A-9-

CA

31A-101-

HOH

41A-103-

HOH

51A-106-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA heptamer
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Drops initially containing 2ul 20 mm sodium cacodylate, 2ul calcium chloride, 2ul potassium chloride, 2 ul 10% PEG, 2ul 1 mM DNA, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→29.11 Å / Num. all: 1246 / Num. obs: 1246 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CrystalCleardata collection
XFITdata reduction
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.11 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.89 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.193 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27918 64 4.9 %RANDOM
Rwork0.23927 ---
obs0.24135 1233 93.85 %-
all-1246 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.9→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 140 2 10 152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021156
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1993239
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_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0271
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1680.243
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.288
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2730.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.212
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1430.23
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 5 -
Rwork0.375 87 -
obs-156 87.62 %

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