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- PDB-6aqw: Crystal Structure of Z-DNA with 6-fold Twinning_Z4A -

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Basic information

Entry
Database: PDB / ID: 6aqw
TitleCrystal Structure of Z-DNA with 6-fold Twinning_Z4A
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: 1.3 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 1.1Nov 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 1.2Oct 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')
G: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
H: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)14,4828
Polymers14,4828
Non-polymers00
Water2,918162
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 area650 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 area640 Å2
ΔGint-5 kcal/mol
Surface area2330 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-5 kcal/mol
Surface area2310 Å2
MethodPISA
4
G: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
H: 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-5 kcal/mol
Surface area2310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.430, 44.000, 35.430
Angle α, β, γ (deg.)90.00, 119.83, 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.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.65 Å3/Da / Density % sol: 25.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Percipient: 200 mM CaCl2, 50 mM Tris-HCl pH 7.0, 10% MPD Reservior: 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 10, 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, L10.274
11L, -K, H20.016
11-H-L, K, H30.099
11-H, -K, H+L40.144
11L, K, -H-L50.34
11H+L, -K, -L60.127
ReflectionResolution: 1.3→31 Å / Num. obs: 22010 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.8
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2242 / CC1/2: 0.752 / % possible all: 98.8

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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: 1.3→30.74 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 3.07 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.012 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18418 1020 4.6 %RANDOM
Rwork0.16805 ---
obs0.16888 20986 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.546 Å2
Baniso -1Baniso -2Baniso -3
1--3.59 Å2-0 Å24.06 Å2
2--12.85 Å20 Å2
3----9.27 Å2
Refinement stepCycle: 1 / Resolution: 1.3→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 960 0 162 1122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0111121
X-RAY DIFFRACTIONr_bond_other_d0.0030.02536
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.1721729
X-RAY DIFFRACTIONr_angle_other_deg1.76131278
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_restr0.0870.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02584
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02272
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_it3.9234.8491121
X-RAY DIFFRACTIONr_scbond_other3.9244.8491120
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8619.2091730
X-RAY DIFFRACTIONr_long_range_B_refined5.04622.2881739
X-RAY DIFFRACTIONr_long_range_B_other4.72921.961680
X-RAY DIFFRACTIONr_rigid_bond_restr3.68831657
X-RAY DIFFRACTIONr_sphericity_free34.741543
X-RAY DIFFRACTIONr_sphericity_bonded20.13551655
LS refinement shellResolution: 1.302→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 44 -
Rwork0.26 981 -
obs--60.87 %

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