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- PDB-2dz7: DNA Octaplex Formation with an I-Motif of A-Quartets: The Revised... -

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Basic information

Entry
Database: PDB / ID: 2dz7
TitleDNA Octaplex Formation with an I-Motif of A-Quartets: The Revised Crystal Structure of d(GCGAAAGC)
ComponentsDNA (5'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3')
KeywordsDNA / A-quartet / DNA octaplex / non-coding DNA / VNTR
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSato, Y. / Mitomi, K. / Sumani, T. / Kondo, J. / Takenaka, A.
CitationJournal: J.Biochem.(Tokyo) / Year: 2006
Title: DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC)
Authors: Sato, Y. / Mitomi, K. / Sunami, T. / Kondo, J. / Takenaka, A.
History
DepositionSep 21, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: 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 / pdbx_struct_conn_angle / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5093
Polymers2,4611
Non-polymers492
Water1,29772
1
A: DNA (5'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3')
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)20,07424
Polymers19,6858
Non-polymers38916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
crystal symmetry operation5_756-x+2,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_646y+1,x-1,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)36.909, 36.909, 64.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-2001-

MG

21A-2003-

HOH

31A-2004-

HOH

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Components

#1: DNA chain DNA (5'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3')


Mass: 2460.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium chloride, magnesium chloride, spermine 4HCl, 2-methyl-2,4-pentanediol, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium chloride11
2magnesium chloride11
3spermine 4HCl11
42-methyl-2,4-pentanediol11
5sodium cacodylate11
6HOH11
7sodium chloride12
8magnesium chloride12
9sodium cacodylate12
10HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→60 Å / Num. obs: 3359 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.3
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UE3(PDB code)

1ue3


Resolution: 1.6→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 772275.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Details: The structure was refined also with Refmac5
RfactorNum. reflection% reflectionSelection details
Rfree0.211 270 9.8 %RANDOM
Rwork0.19 ---
obs0.19 2764 88 %-
all-3359 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.6892 Å2 / ksol: 0.455882 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å20 Å2
2--3.65 Å20 Å2
3----7.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 164 2 72 238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.47
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 34 10.1 %
Rwork0.2 304 -
obs--67.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4mg_o6.param

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