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Entry
Database: PDB / ID: 5ebi
TitleCrystal structure of a DNA-RNA chimera in complex with Ba2+ ions: a case of unusual multi-domain twinning
ComponentsDNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
KeywordsDNA/RNA CHIMERA / DNA-RNA CHIMERA COMPLEX / Z-DNA / Z-RNA / SELF-COMPLEMENTARY DUPLEX / LEFT-HANDED Z-TYPE DUPLEX / MULTI-DOMAIN TWINNING / DETECTION / TWIN PSEUDOSYMMETRY
Function / homology: / DNA/RNA hybrid
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsGilski, M. / Drozdzal, P. / Kierzek, R. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Center2013/10/M/NZ1/00251 Poland
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Atomic resolution structure of a chimeric DNA-RNA Z-type duplex in complex with Ba(2+) ions: a case of complicated multi-domain twinning.
Authors: Gilski, M. / Drozdzal, P. / Kierzek, R. / Jaskolski, M.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.
Authors: Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M.
#2: Journal: J. Biol. Inorg. Chem. / Year: 2015
Title: High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations.
Authors: Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M.
#3: Journal: Biochemistry / Year: 1989
Title: Effects of the O2' hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)-[Z-DNA].
Authors: Teng, M.K. / Liaw, Y.C. / van der Marel, G.A. / van Boom, J.H. / Wang, A.H.
#4: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2002
Title: Crystallization of the Zalpha domain of the human editing enzyme ADAR1 complexed with a DNA-RNA chimeric oligonucleotide in the left-handed Z-conformation.
Authors: Brown, B.A. / Athanasiadis, A. / Hanlon, E.B. / Lowenhaupt, K. / Wilbert, C.M. / Rich, A.
#5: Journal: Nucleic Acids Res. / Year: 2011
Title: High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.
Authors: Brzezinski, K. / Brzuszkiewicz, A. / Dauter, M. / Kubicki, M. / Jaskolski, M. / Dauter, Z.
#6: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2007
Title: Structure determination by multiwavelength anomalous diffraction of aclacinomycin oxidoreductase: indications of multidomain pseudomerohedral twinning.
Authors: Sultana, A. / Alexeev, I. / Kursula, I. / Mantsala, P. / Niemi, J. / Schneider, G.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
B: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
C: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
D: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
E: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
F: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
G: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
H: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,06324
Polymers14,8668
Non-polymers2,19716
Water4,035224
1
A: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
B: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6789
Polymers3,7162
Non-polymers9617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-24 kcal/mol
Surface area2860 Å2
MethodPISA
2
C: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
D: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2666
Polymers3,7162
Non-polymers5494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-23 kcal/mol
Surface area2840 Å2
MethodPISA
3
E: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
F: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1285
Polymers3,7162
Non-polymers4123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-27 kcal/mol
Surface area2840 Å2
MethodPISA
4
G: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
H: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9914
Polymers3,7162
Non-polymers2752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-27 kcal/mol
Surface area2840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.720, 44.100, 35.720
Angle α, β, γ (deg.)90.00, 119.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA/RNA hybrid
DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3')


Mass: 1858.205 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.65 Å3/Da / Density % sol: 25.44 %
Crystal growTemperature: 292 K
Details: A 1.5 MM WATER SOLUTION OF DNA-RNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 80 MM NACL, 20 MM BACL2, 40 MM SODIUM CACODYLATE AND EQUILIBRATED AGAINST 35% MPD, PH 6.0, VAPOR ...Details: A 1.5 MM WATER SOLUTION OF DNA-RNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 80 MM NACL, 20 MM BACL2, 40 MM SODIUM CACODYLATE AND EQUILIBRATED AGAINST 35% MPD, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.0K
Method: vapor diffusion, hanging drop / pH: 6
Details: A 1.5 MM WATER SOLUTION OF DNA-RNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 80 MM NACL, 20 MM BACL2, 40 MM SODIUM CACODYLATE AND EQUILIBRATED AGAINST 35% MPD, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8266 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 8, 2012
RadiationMonochromator: Double crystal Si (111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.279
11L, -K, H20.103
11H+L, -K, -L30.275
11L, K, -H-L40.113
11-H-L, K, H50.11
11-H, -K, H+L60.121
ReflectionResolution: 1.09→30.94 Å / Num. all: 40052 / Num. obs: 40052 / % possible obs: 99.4 % / Redundancy: 5.84 % / Biso Wilson estimate: 11.719 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.07
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.12 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P4J

3p4j


Resolution: 1.09→30.94 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0 / SU B: 0.355 / SU ML: 0.009 / Cross valid method: FREE R-VALUE / ESU R: 0.006
StereochEM target val spec case: PHOSPHATE AND GLYCOSIDIC ANGLES ACCORDING TO PDB MODEL 3P4J
Stereochemistry target values: CLOWNEY, GELBIN & PARKINSON
Details: ANISOTROPIC ATOMIC DISPLACEMENT PARAMETERS WERE USED. HYDROGEN ATOMS WERE ADDED AT RIDING POSITION THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL-MATRIX LEAST-SQUARES PROCEDURE AND ALL REFLECTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.169 101 2.55 %Using the 'thin resolution shells' method
Rwork0.115 ---
obs0.11361 40051 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.814 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-13.14 Å2
2---0.49 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.09→30.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 984 16 224 1224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.011159
X-RAY DIFFRACTIONr_bond_other_d0.0020.02533
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.2681812
X-RAY DIFFRACTIONr_angle_other_deg1.69831286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.140.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02584
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02272
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6481.1051159
X-RAY DIFFRACTIONr_scbond_other3.6491.1051158
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3671.6831806
X-RAY DIFFRACTIONr_long_range_B_refined5.16411.7061825
X-RAY DIFFRACTIONr_long_range_B_other4.39111.0461676
X-RAY DIFFRACTIONr_rigid_bond_restr12.44531692
X-RAY DIFFRACTIONr_sphericity_free27.212537
X-RAY DIFFRACTIONr_sphericity_bonded15.42951774
LS refinement shellResolution: 1.09→1.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 101 -
Rwork0.175 2909 -
obs--99.08 %

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