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- PDB-5jzq: Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA r... -

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Basic information

Entry
Database: PDB / ID: 5jzq
TitleUltrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals massive presence of multiple conformations
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA duplex / self-complementary duplex / centrosymmetric space group / DNA enantiomer / racemate / L-ribose nucleic acid / disorder / macromolecular phase problem / ab initio methods / dual-space methods
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.78 Å
AuthorsDrozdzal, P. / Gilski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2013/10/M/NZ1/00251 Poland
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations.
Authors: Drozdzal, P. / Gilski, M. / Jaskolski, M.
#1: Journal: J. Am. Chem. Soc. / Year: 1993
Title: Structural characteristics of enantiomorphic DNA: crystal analysis of racemates of the d(CGCGCG) duplex
Authors: Doi, M. / Inoue, M. / Tomoo, K. / Ishida, T. / Ueda, Y. / Akagi, M. / Urata, H.
#2: 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.
#3: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2001
Title: Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.
Authors: Dauter, Z. / Adamiak, D.A.
#4: 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.
#5: 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.
#6: 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.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 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 1.3May 8, 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
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_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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,6935
Polymers3,6202
Non-polymers733
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-18 kcal/mol
Surface area2440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.300, 17.610, 36.490
Angle α, β, γ (deg.)90.00, 106.73, 90.00
Int Tables number15
Space group name H-MC12/c1
Components on special symmetry positions
IDModelComponents
11A-102-

MG

21A-241-

HOH

31A-244-

HOH

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Components

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


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: racemic mixture of D- and L-oligodeoxyribonucleotides
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1.74 Å3/Da / Density % sol: 28.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 MM WATER SOLUTION OF DNA MIXED 1:1 WITH 0.2 M (NH4)2OAc, 0.15 M Mg(OAc)2, 0.05 M HEPES SODIUM PH 7.0 AND 5% (W/V) PEG 4000 AND EQUILIBRATED AGAINST 0.5 ML of 5% (V/V) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.7999 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 29, 2014
RadiationMonochromator: Double crystal Si (111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 0.78→38.93 Å / Num. obs: 53660 / % possible obs: 95.5 % / Redundancy: 9.01 % / Biso Wilson estimate: 12.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0339 / Net I/σ(I): 25.75
Reflection shellResolution: 0.78→0.8 Å / Redundancy: 4.54 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.12 / % possible all: 88.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XPREPdata reduction
SHELXSphasing
SHELXL2014/7refinement
SHELXL-97refinement
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.78→38.93 Å / Cross valid method: FREE R-VALUE
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
Rfree0.1425 982 1.83 %RANDOM
Rwork0.1386 ---
all0.1383 ---
obs0.1399 53660 95.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201
Refine analyzeNum. disordered residues: 45 / Occupancy sum hydrogen: 133 / Occupancy sum non hydrogen: 339.1
Refinement stepCycle: LAST / Resolution: 0.78→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 3 142 385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0169
X-RAY DIFFRACTIONs_angle_d1.776
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.008
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1275
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0652
X-RAY DIFFRACTIONs_approx_iso_adps0.1149

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