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- PDB-5bz7: X-ray crystal structure of a continuously hydrogen bonded 14mer D... -

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Basic information

Entry
Database: PDB / ID: 5bz7
TitleX-ray crystal structure of a continuously hydrogen bonded 14mer DNA lattice.
ComponentsDNA (5'-D(*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*GP*AP*GP*A)-3')
KeywordsDNA / 3D DNA lattice / 14mer DNA / Self assembly
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSaoji, M. / Paukstelis, P.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.
Authors: Saoji, M. / Paukstelis, P.J.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 2023Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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 (5'-D(*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4423
Polymers4,3931
Non-polymers492
Water23413
1
A: DNA (5'-D(*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*GP*AP*GP*A)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8836
Polymers8,7862
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1520 Å2
ΔGint-15 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.013, 26.013, 122.022
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*GP*AP*GP*A)-3')


Mass: 4392.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, sitting drop
Details: 120mM Magnesium Formate 50mM Lithium Chloride 10% MPD

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.03→22.53 Å / Num. obs: 3436 / % possible obs: 99.4 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 13.9
Reflection shellResolution: 2.03→2.09 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHENIXrefinement
Aimlessdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BXW

5bxw


Resolution: 2.03→22.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.263 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2934 344 10 %RANDOM
Rwork0.23352 ---
obs0.23875 3092 97.78 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.957 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.03→22.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 293 2 13 308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.011331
X-RAY DIFFRACTIONr_bond_other_d0.0010.02158
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.15511
X-RAY DIFFRACTIONr_angle_other_deg3.3773374
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_restr0.1630.242
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02176
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0270
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_it7.6735.896331
X-RAY DIFFRACTIONr_scbond_other7.6625.892332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.3438.885511
X-RAY DIFFRACTIONr_long_range_B_refined11.11154.806483
X-RAY DIFFRACTIONr_long_range_B_other11.10654.773483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.538 22 -
Rwork0.502 206 -
obs--91.2 %

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