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- PDB-1p25: Crystal structure of nickel(II)-d(GGCGCC)2 -

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Basic information

Entry
Database: PDB / ID: 1p25
TitleCrystal structure of nickel(II)-d(GGCGCC)2
Components5'-D(*GP*GP*CP*GP*CP*C)-3'
KeywordsDNA / B-DNA / nickel binding
Function / homologyNICKEL (II) ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLabiuk, S.L. / Delbaere, L.T. / Lee, J.S.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2003
Title: Cobalt(II), nickel(II) and zinc(II) do not bind to intra-helical N(7) guanine positions in the B-form crystal structure of d(GGCGCC)
Authors: Labiuk, S.L. / Delbaere, L.T. / Lee, J.S.
History
DepositionApr 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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.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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*GP*CP*GP*CP*C)-3'
B: 5'-D(*GP*GP*CP*GP*CP*C)-3'
C: 5'-D(*GP*GP*CP*GP*CP*C)-3'
D: 5'-D(*GP*GP*CP*GP*CP*C)-3'
E: 5'-D(*GP*GP*CP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,34410
Polymers9,0515
Non-polymers2935
Water45025
1
A: 5'-D(*GP*GP*CP*GP*CP*C)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)3,7384
Polymers3,6202
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
2
B: 5'-D(*GP*GP*CP*GP*CP*C)-3'
C: 5'-D(*GP*GP*CP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7384
Polymers3,6202
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: 5'-D(*GP*GP*CP*GP*CP*C)-3'
E: 5'-D(*GP*GP*CP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7384
Polymers3,6202
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.99, 68.99, 56.18
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

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


Mass: 1810.205 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: Synthesized by AlphaDNA (Quebec, PQ, Canada)
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.79 Å3/Da / Density % sol: 67.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: DNA, TAPS-HCl, NiCl2, MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Taps-HCl11
2NiCl211
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mMhexamer1drop
240 mMTAPS-HCl1droppH8.0
33.75 mM1dropNiCl2
410 %1drop
540 mMTAPS-HCl1reservoirpH8.0
63.75 mM1reservoirNiCl2
735 %MPD1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→26 Å / Num. all: 3217 / Num. obs: 3217 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 47.9 Å2 / Rsym value: 0.09 / Net I/σ(I): 22
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.6 / % possible all: 80.6
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. measured all: 180742 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 80.6 % / Rmerge(I) obs: 0.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY BD0040

Resolution: 2.9→15 Å / Isotropic thermal model: Grouped B-values / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 261 9 %random
Rwork0.223 ---
all0.2281 2924 --
obs0.228 2706 --
Displacement parametersBiso mean: 29.4 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 940 5 25 970
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg3.996
X-RAY DIFFRACTIONx_dihedral_angle_d32.665
X-RAY DIFFRACTIONx_improper_angle_d1.305
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg32.665
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.305

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