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- PDB-446d: STRUCTURE OF THE OLIGONUCLEOTIDE D(CGTATATACG) AS A SITE SPECIFIC... -

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Basic information

Entry
Database: PDB / ID: 446d
TitleSTRUCTURE OF THE OLIGONUCLEOTIDE D(CGTATATACG) AS A SITE SPECIFIC COMPLEX WITH NICKEL IONS
ComponentsDNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3')
KeywordsDNA / TRIPLE HELIX / NICKEL BINDING
Function / homologyNICKEL (II) ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsAbrescia, N.G.A. / Malinina, L. / Gonzaga, L.F. / Huynh-Dinh, T. / Neidle, S. / Subirana, J.A.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: Structure of the oligonucleotide d(CGTATATACG) as a site-specific complex with nickel ions.
Authors: Abrescia, N.G. / Malinina, L. / Fernandez, L.G. / Huynh-Dinh, T. / Neidle, S. / Subirana, J.A.
History
DepositionJan 15, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 18, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,70413
Polymers12,1764
Non-polymers5289
Water1,09961
1
A: DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4408
Polymers6,0882
Non-polymers3526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2645
Polymers6,0882
Non-polymers1763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.460, 52.460, 101.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

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


Mass: 3044.017 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ni
#3: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMDNA duplex1drop
24 %MPD1drop
310 mM1dropNiCl2
48 %MPD1reservoir
525 mMNa cacodylate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 3841 / % possible obs: 99.4 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.405 / % possible all: 69.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 3015 / % possible obs: 94.2 % / Num. measured all: 59339 / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.253 258 -
Rwork0.204 --
obs0.204 2427 82.33 %
all-3015 -
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 762 9 61 832
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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