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- PDB-5f9i: Crystal Structure of rich-AT DNA 20mer -

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Basic information

Entry
Database: PDB / ID: 5f9i
TitleCrystal Structure of rich-AT DNA 20mer
ComponentsDNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')
KeywordsDNA / Long DNA / crossed DNA / oligonucleotide / 20mer / AT-rich
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGarcia, S. / Acosta-Reyes, F.J. / Saperas, N. / Campos, J.L.
Funding support Spain, 2items
OrganizationGrant numberCountry
MICIN - FEDERBFU-2009-10380 Spain
Generalitat de CatalunyaSRG2009-1208 Spain
CitationJournal: To Be Published
Title: Crystal Structure of rich-AT DNA 20mer
Authors: Garcia, S. / Acosta-Reyes, F.J. / Saperas, N. / Campos, J.L.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')
C: DNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')
D: DNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,5324
Polymers24,5324
Non-polymers00
Water724
1
A: DNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,2662
Polymers12,2662
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-9 kcal/mol
Surface area7270 Å2
MethodPISA
2
C: DNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')
D: DNA (5'-D(*CP*CP*AP*AP*TP*AP*AP*TP*CP*GP*CP*GP*AP*TP*TP*AP*TP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,2662
Polymers12,2662
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-9 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.647, 26.340, 76.434
Angle α, β, γ (deg.)90.00, 95.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6132.991 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.48 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Na Cacodylate pH 6.5, MgCl2 ,MPD 45% / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 5042 / % possible obs: 98.79 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.91
Reflection shellResolution: 3→3.24 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.45 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDS20141118data reduction
XDS20141118data scaling
MOLREP11.4.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 39.914 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25019 156 3.1 %RANDOM
Rwork0.22582 ---
obs0.22662 4886 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.509 Å2
Baniso -1Baniso -2Baniso -3
1--6.53 Å20 Å2-1.69 Å2
2--2.78 Å20 Å2
3---4.02 Å2
Refinement stepCycle: 1 / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1628 0 4 1632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0111824
X-RAY DIFFRACTIONr_bond_other_d0.0040.02908
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.1772808
X-RAY DIFFRACTIONr_angle_other_deg1.93432156
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_restr0.0990.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02376
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_it7.4616.6191824
X-RAY DIFFRACTIONr_scbond_other7.4596.6211823
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.7729.9352809
X-RAY DIFFRACTIONr_long_range_B_refined14.92462.2078139
X-RAY DIFFRACTIONr_long_range_B_other14.92462.2048140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 7 -
Rwork0.264 342 -
obs--99.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.88492.7895-0.10381.6791-0.06770.00680.1788-0.15790.09150.0811-0.16090.01040.0004-0.0003-0.01790.0265-0.037-0.00040.14790.01540.070410.68352.227228.0971
24.80432.77580.23551.61040.1170.22940.1808-0.12450.08920.1114-0.10380.05220.02650.001-0.0770.0212-0.03490.01830.13940.01550.145711.00742.366128.3122
36.3032-2.19490.28610.8276-0.07820.04290.0851-0.19980.0007-0.0533-0.02010.0143-0.0092-0.0332-0.0650.04330.08060.03390.2130.00650.1958-14.8387-2.54759.9446
45.3474-1.923-0.07280.7798-0.00470.01650.0789-0.0990.091-0.0253-0.0392-0.0151-0.01160.0139-0.03970.04090.06840.02250.203-0.01830.2509-15.112-2.52679.7317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2B21 - 40
3X-RAY DIFFRACTION3C1 - 20
4X-RAY DIFFRACTION4D21 - 40

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