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- PDB-1g3v: CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2 -

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Basic information

Entry
Database: PDB / ID: 1g3v
TitleCRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2
Components5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
KeywordsDNA / nickel binding / B-DNA
Function / homologyNICKEL (II) ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsSubirana, J.A. / Abrescia, N.G.A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2002
Title: Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2.
Authors: Abrescia, N.A. / Huynh-Dinh, T. / Subirana, J.A.
History
DepositionOct 25, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
C: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,65012
Polymers12,1804
Non-polymers4708
Water93752
1
A: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3837
Polymers6,0902
Non-polymers2935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2665
Polymers6,0902
Non-polymers1763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.031, 53.031, 97.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 3045.004 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: DNA, NiCl2, MPD, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Components of the solutions
IDNameCrystal-IDSol-ID
1DNA11
2NiCl211
3MPD11
4MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 mMprotein1drop
210 mM1dropNiCl2
34 %1drop
510 %MPD1reservoir
4sodium cacodylate1droppH6.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9058
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9058 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 2843 / Num. obs: 2843 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 15.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.3
Reflection shellResolution: 3.1→3.18 Å / Rmerge(I) obs: 0.49 / Num. unique all: 213 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 79.3 % / Num. measured all: 43286 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 50.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.1→8 Å / σ(F): 1
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
Details: maximum likelihood target function
RfactorNum. reflection% reflectionSelection details
Rfree0.27 230 -random
Rwork0.209 ---
all-2472 --
obs-2472 94.2 %-
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 769 8 52 829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 8 Å / σ(F): 1 / Rfactor all: 0.252 / Rfactor obs: 0.209 / Rfactor Rfree: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.1

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