PDB-1r2o: d(GCATGCT) + Ni2+

Basic information

• Entry: Database: PDB / ID: 1r2o
• Title: d(GCATGCT) + Ni2+
• Components: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'
• Keywords: DNA / METAL ION / DNA QUADRUPLEX
• Function / homology: NICKEL (II) ION / DNA
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
• Authors: Cardin, J.C. / Gan, Y. / Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Moraes, M.I.A.
• Citation: Journal: To be published; Title: Metal Ion Distribution and Stabilization of the DNA Quadruplex Structure Formed by d(GCATGCT); Authors: Cardin, J.C. / Gan, Y. / Thorpe, J.H. / Teixeira, S.C.M. / Gale, B.C. / Moraes, M.I.A.

History

Deposition	Sep 29, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Derived calculations Category: 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 / _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.ptnr1_symmetry / _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_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.ptnr1_symmetry / _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

Assembly

Deposited unit

X: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'

hetero molecules

Summary:

• 2.17 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	2,172	2
Polymers	2,113	1
Non-polymers	59	1
Water	144	8

1

X: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'

hetero molecules

X: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'

hetero molecules

X: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'

hetero molecules

X: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'

hetero molecules

Summary:

• defined by author
• 8.69 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,688	8
Polymers	8,454	4
Non-polymers	235	4
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_555	-x,-y,z	1
crystal symmetry operation	9_555	-x,-x+y,-z+1/3	1
crystal symmetry operation	12_555	x,x-y,-z+1/3	1

Unit cell

Length a, b, c (Å)	24.807, 24.807, 92.081
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	180
Space group name H-M	P6222

Components on special symmetry positions

ID	Model	Components
1	1	X-7- DT
2	1	X-7- DT
3	1	X-201- HOH

Components

#1: DNA chain

X 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'

Details:

Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically

#2: Chemical

X-101 ChemComp-NI / NICKEL (II) ION

Details:

Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 1.86 ų/Da / Density % sol: 34.03 %
• Crystal grow: Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.7 ; Details: sodium cacodylate, nickel dichloride, potassium chloride, MPD, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	sodium cacodylate	1	1
2	nickel dichloride	1	1
3	potassium chloride	1	1
4	MPD	1	1
5	H2O	1	1
6	sodium cacodylate	1	2
7	nickel dichloride	1	2
8	MPD	1	2
9	H2O	1	2

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126 Å
• Detector: Type: MARRESEARCH / Detector: CCD / Date: Dec 15, 2002
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.8126 Å / Relative weight: 1
• Reflection: Resolution: 2.38→30.71 Å / Num. obs: 857 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.47 % / B_iso Wilson estimate: 31.357 Ų / R_merge(I) obs: 0.082 / Net I/σ(I): 9.9
• Reflection shell: Resolution: 2.38→2.51 Å / Redundancy: 17.1 % / R_merge(I) obs: 0.216 / Mean I/σ(I) obs: 4 / Num. unique all: 119 / % possible all: 99.9

Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
XTALVIEW		refinement

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→30.71 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.897 / SU B: 4.499 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.661 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.24596	22	5.7 %	RANDOM
Rwork	0.2244	-	-	-
obs	0.22558	801	99.3 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 30.848 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.26 Å2	0.13 Å2	0 Å2
2-	-	0.26 Å2	0 Å2
3-	-	-	-0.39 Å2

Refinement step

Cycle: LAST / Resolution: 2.38→30.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	160	1	8	169

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	178
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	81
X-RAY DIFFRACTION	r_angle_refined_deg	2.467	3	273
X-RAY DIFFRACTION	r_angle_other_deg	1.191	3	202
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	24
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	83
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3
X-RAY DIFFRACTION	r_nbd_refined	0.121	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	62
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	45
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	2
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.159	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.233	0.2	9
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.103	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it	2.173	3	178
X-RAY DIFFRACTION	r_scangle_it	3.214	4.5	273
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.38→2.445 Å / Total num. of bins used: 20 /

	Rfactor	Num. reflection
Rfree	0.19	7
Rwork	0.179	52