PDB-4j2i: Multiple crystal structures of an all-AT DNA dodecamer stabilized...

ID or keywords:

Entry

Database: PDB / ID: 4j2i

Title

Multiple crystal structures of an all-AT DNA dodecamer stabilized by weak interactions

Components

5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

Keywords

DNA / oligonucleotides / weak interactions / AT-rich DNA

Function / homology

DNA / DNA (> 10)

Function and homology information

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.98 Å

Authors

Acosta-Reyes, F.J. / Subirana, J.A. / Pous, J. / Sanchez, R. / Condom, N. / Baldini, R. / Malinina, L. / Campos, J.L.

Citation

Journal: Biopolymers / Year: 2015
Title: Polymorphic crystal structures of an all-AT DNA dodecamer.
Authors: Acosta-Reyes, F.J. / Subirana, J.A. / Pous, J. / Sanchez-Giraldo, R. / Condom, N. / Baldini, R. / Malinina, L. / Campos, J.L.

History

Deposition	Feb 4, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 15, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4j2i_validation.pdf.gz	416 KB	Display	wwPDB validaton report
Full document	4j2i_full_validation.pdf.gz	416.6 KB	Display
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Related structure data

Related structure data	4hw1C C: citing same article (ref.)
Similar structure data	2l8q-d 2mhz-d 2hli-d 5l2g-d 1n2w-d 2hkb-d 5uz1-d 4hw1-1 6alt-d 5uz3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

4hw1C

C: citing same article (ref.)

Similar structure data

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PDB pages	PDBj / wwPDB / NCBI
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similarity (1)
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similarity (1)
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Deposited unit

A: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

B: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

C: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

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

E: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

F: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

G: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

H: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

29.3 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

B: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

defined by author&software
7.32 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

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

defined by author&software
7.32 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

F: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

defined by author&software
7.32 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

H: 5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3'

defined by author&software
7.32 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.400, 27.945, 159.715
Angle α, β, γ (deg.)	90.00, 103.10, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	H-102- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: DA / Beg label comp-ID: DA / End auth comp-ID: DT / End label comp-ID: DT / Refine code: _ / Label seq-ID: 1 - 12

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID	Auth seq-ID
1	1	A	A	1 - 12
2	1	B	B	13 - 24
1	2	A	A	1 - 12
2	2	C	C	1 - 12
1	3	A	A	1 - 12
2	3	D	D	13 - 24
1	4	A	A	1 - 12
2	4	E	E	1 - 12
1	5	A	A	1 - 12
2	5	F	F	13 - 24
1	6	A	A	1 - 12
2	6	G	G	1 - 12
1	7	A	A	1 - 12
2	7	H	H	13 - 24
1	8	B	B	13 - 24
2	8	C	C	1 - 12
1	9	B	B	13 - 24
2	9	D	D	13 - 24
1	10	B	B	13 - 24
2	10	E	E	1 - 12
1	11	B	B	13 - 24
2	11	F	F	13 - 24
1	12	B	B	13 - 24
2	12	G	G	1 - 12
1	13	B	B	13 - 24
2	13	H	H	13 - 24
1	14	C	C	1 - 12
2	14	D	D	13 - 24
1	15	C	C	1 - 12
2	15	E	E	1 - 12
1	16	C	C	1 - 12
2	16	F	F	13 - 24
1	17	C	C	1 - 12
2	17	G	G	1 - 12
1	18	C	C	1 - 12
2	18	H	H	13 - 24
1	19	D	D	13 - 24
2	19	E	E	1 - 12
1	20	D	D	13 - 24
2	20	F	F	13 - 24
1	21	D	D	13 - 24
2	21	G	G	1 - 12
1	22	D	D	13 - 24
2	22	H	H	13 - 24
1	23	E	E	1 - 12
2	23	F	F	13 - 24
1	24	E	E	1 - 12
2	24	G	G	1 - 12
1	25	E	E	1 - 12
2	25	H	H	13 - 24
1	26	F	F	13 - 24
2	26	G	G	1 - 12
1	27	F	F	13 - 24
2	27	H	H	13 - 24
1	28	G	G	1 - 12
2	28	H	H	13 - 24

NCS ensembles :

#1: DNA chain	5'-D(APAPTPAPAPAPTPTPTPAPTPT)-3' Mass: 3659.440 Da / Num. of mol.: 8 / Source method: obtained synthetically
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.88 %
Crystal grow	Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ni, Spermine, Sodium cacodilate, 36% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: BM16 / Wavelength: 0.91986 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 19, 2005 / Details: Mirrors

Radiation

Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.91986 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.502
1	1	-H, -K, H+L	2	0.498

Reflection

Resolution: 2.98→26.5 Å / Num. all: 7242 / Num. obs: 6641 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / R_merge(I) obs: 0.138 / Net I/σ(I): 5.9

Reflection shell

Resolution: 2.98→3.14 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.216 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
AMoRE		phasing
REFMAC	5.8.0024	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.98→26.5 Å / Cor.coef. F_o:F_c: 0.916 / Cor.coef. F_o:F_c free: 0.901 / SU B: 14.714 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28729	292	4.4 %	RANDOM
R_work	0.26963	-	-	-
obs	0.27031	6348	99.02 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 52.175 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-57.27 Å²	-0 Å²	-0.41 Å²
2-	-	-30.35 Å²	-0 Å²
3-	-	-	87.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.98→26.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	1944	0	17	1961

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.01	2278
X-RAY DIFFRACTION	r_bond_other_d	0.014	0.02	1112
X-RAY DIFFRACTION	r_angle_refined_deg	1.075	1.188	3344
X-RAY DIFFRACTION	r_angle_other_deg	4.638	3	2648
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	15.23	15	48
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.306	0.275	384
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1088
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	368
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

LS refinement shell

Resolution: 2.982→3.06 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.42	27	-
R_work	0.419	439	-
obs	-	-	96.48 %

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