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- PDB-5zt2: Crystal structure of CCG DNA repeats at 1.66 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5zt2
TitleCrystal structure of CCG DNA repeats at 1.66 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 / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66002164937 Å
AuthorsHou, M.H. / Wu, P.C. / Satange, R.B. / Chen, Y.W.
Citation
Journal: To Be Published
Title: Crystallographic analysis of conformational change in CCG repeats into i-motif and unusual DNA duplex in presence and absence of CoII(Chro)2 complex
Authors: Hou, M.H.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Structural basis for the identification of an i-motif tetraplex core with a parallel-duplex junction as a structural motif in CCG triplet repeats.
Authors: Chen, Y.W. / Jhan, C.R. / Neidle, S. / Hou, M.H.
History
DepositionMay 1, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 15, 2019ID: 4QNO
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Mar 27, 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
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.ptnr2_auth_seq_id

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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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4133
Polymers3,2951
Non-polymers1182
Water1,06359
1
A: DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,8266
Polymers6,5902
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)38.299, 38.299, 54.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

21A-244-

HOH

31A-257-

HOH

41A-259-

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: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50mM Sodium cacodylate, 1mM Magnesium chloride, 5% MPD, 2mM Cobalt(II) chloride, 1mM Chromomycin A3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1.60572, 1.56518, 1.60490
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 18, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.605721
21.565181
31.60491
ReflectionResolution: 1.66→30 Å / Num. obs: 3447 / % possible obs: 96.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 16.5972142739 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 41.724
Reflection shellResolution: 1.66→1.72 Å / Rmerge(I) obs: 0.272 / Num. unique obs: 632

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.66002164937→12.4437277752 Å / SU ML: 0.20873662372 / Cross valid method: FREE R-VALUE / σ(F): 0.00486031212139 / Phase error: 30.6258331204
RfactorNum. reflection% reflection
Rfree0.255296437209 345 10.0087032202 %
Rwork0.233436819255 --
obs0.235638826004 3447 67.0883612301 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.7353127997 Å2
Refinement stepCycle: LAST / Resolution: 1.66002164937→12.4437277752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 218 2 59 279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643641523394243
X-RAY DIFFRACTIONf_angle_d0.691642373619372
X-RAY DIFFRACTIONf_chiral_restr0.029969851243243
X-RAY DIFFRACTIONf_plane_restr0.0030829249549811
X-RAY DIFFRACTIONf_dihedral_angle_d31.4914944287106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.71920.3224346464951580.2801596789131424X-RAY DIFFRACTION63.1284916201
2.0898-12.44410.2334588044561870.21878117981678X-RAY DIFFRACTION70.8855948309

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