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- PDB-6aqt: Crystal Structure of Z-DNA with 6-fold Twinning_Z3A -

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Basic information

Entry
Database: PDB / ID: 6aqt
TitleCrystal Structure of Z-DNA with 6-fold Twinning_Z3A
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / twinning
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsLuo, Z. / Dauter, Z. / Gilski, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Four highly pseudosymmetric and/or twinned structures of d(CGCGCG)2 extend the repertoire of crystal structures of Z-DNA.
Authors: Luo, Z. / Dauter, Z. / Gilski, M.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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')
C: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)10,8616
Polymers10,8616
Non-polymers00
Water1,856103
1
A: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-5 kcal/mol
Surface area2310 Å2
MethodPISA
2
C: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-6 kcal/mol
Surface area2320 Å2
MethodPISA
3
E: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-6 kcal/mol
Surface area2310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.920, 42.890, 30.950
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 chain
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Mass: 1810.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.64 Å3/Da / Density % sol: 24.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Precipitant: 200 mM MgCl2, 50 mM Tris-HCl pH 7.0, 10% MPD. Well solution: 50% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9756 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.173
11-H, -K, H+L20.205
11H+L, -K, -L30.163
11-H-L, K, H40.116
11L, K, -H-L50.146
11L, -K, H60.198
ReflectionResolution: 1.05→27 Å / Num. obs: 32555 / % possible obs: 99 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.7
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3031 / CC1/2: 0.74 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P4J

3p4j


Resolution: 1.05→26.81 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.732 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.008 / ESU R Free: 0.009 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23102 1408 4.3 %RANDOM
Rwork0.1935 ---
obs0.19527 31129 98.63 %-
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: 20.15 Å2
Baniso -1Baniso -2Baniso -3
1--5.15 Å2-0 Å2-0.11 Å2
2--8.56 Å20 Å2
3----3.4 Å2
Refinement stepCycle: 1 / Resolution: 1.05→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 720 0 103 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.011814
X-RAY DIFFRACTIONr_bond_other_d0.0020.02402
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.1491248
X-RAY DIFFRACTIONr_angle_other_deg1.7043946
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_restr0.1190.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02438
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02204
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_it4.1313.926814
X-RAY DIFFRACTIONr_scbond_other4.1343.925813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7387.4681249
X-RAY DIFFRACTIONr_long_range_B_refined4.35617.1331221
X-RAY DIFFRACTIONr_long_range_B_other4.0916.8721196
X-RAY DIFFRACTIONr_rigid_bond_restr3.89831216
X-RAY DIFFRACTIONr_sphericity_free26.862536
X-RAY DIFFRACTIONr_sphericity_bonded12.73751197
LS refinement shellResolution: 1.048→1.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 104 -
Rwork0.206 2052 -
obs--86.48 %

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