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- PDB-5dev: High resolution structure of CCG DNA repeats at 1.71 angstrom res... -

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Basic information

Entry
Database: PDB / ID: 5dev
TitleHigh resolution structure of CCG DNA repeats at 1.71 angstrom resolution
ComponentsDNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / DNA structures / i-motifs / neurological disease / tetraplex structures
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsHou, M.H. / Jhan, C.R.
CitationJournal: To Be Published
Title: High resolution structure of CCG DNA repeats at 1.71 angstrom resolution
Authors: Hou, M.H. / Jhan, C.R.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)3,2951
Polymers3,2951
Non-polymers00
Water1,08160
1
A: DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')

A: DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)6,5902
Polymers6,5902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)38.228, 38.228, 54.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-144-

HOH

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Components

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


Mass: 3295.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM Sodium cacodylate, 1 mM magnesium chloride, 3% 2-methylpentane-2,4-diol, 0.5 mM Cobalt(II) chloride

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2014
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→30 Å / Num. obs: 4687 / % possible obs: 99.6 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 67.391
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data collection
PHENIX1.8.4-1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→27.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.156 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 216 4.6 %RANDOM
Rwork0.227 ---
obs0.23 4475 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.71→27.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 218 0 60 278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.012243
X-RAY DIFFRACTIONr_bond_other_d0.0550.02112
X-RAY DIFFRACTIONr_angle_refined_deg3.7531.313372
X-RAY DIFFRACTIONr_angle_other_deg2.343257
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_restr0.150.233
X-RAY DIFFRACTIONr_gen_planes_refined0.0340.02131
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0262
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_it5.6053.927243
X-RAY DIFFRACTIONr_scbond_other5.5943.925244
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2655.908372
X-RAY DIFFRACTIONr_long_range_B_refined7.96740.168352
X-RAY DIFFRACTIONr_long_range_B_other7.91739.842335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 21 -
Rwork0.331 311 -
obs--100 %

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