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- PDB-5fhl: Extensive amphimorphism in DNA: Three stable conformations for th... -

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Basic information

Entry
Database: PDB / ID: 5fhl
TitleExtensive amphimorphism in DNA: Three stable conformations for the decadeoxynucleotide d(GCATGCATGC)
ComponentsDNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
KeywordsDNA / decamer / amphimorphism / A-type helix
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.791 Å
AuthorsThirugnanasambandam, A. / Karthik, S. / Gautham, N.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC).
Authors: Thirugnanasambandam, A. / Karthik, S. / Artheswari, G. / Gautham, N.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,0451
Polymers3,0451
Non-polymers00
Water1448
1
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area960 Å2
ΔGint-3 kcal/mol
Surface area3700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.965, 37.965, 77.195
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.64 Å3/Da / Density % sol: 53.36 % / Description: hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 mM DNA, 50 mM sodium cacodylate buffer, 5 mM spermine, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2014 / Details: Bent collimating mirror
RadiationMonochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.79→30.25 Å / Num. obs: 3435 / % possible obs: 99.6 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 41.38
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MxCuBE2data collection
XDSJan 10, 2014data processing
XSCALEJan 10, 2014data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VTB

1vtb


Resolution: 1.791→30.249 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 344 10.01 %Random selection
Rwork0.2172 ---
obs0.2202 3435 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.791→30.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 0 8 210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014226
X-RAY DIFFRACTIONf_angle_d0.955347
X-RAY DIFFRACTIONf_dihedral_angle_d13.34296
X-RAY DIFFRACTIONf_chiral_restr0.05139
X-RAY DIFFRACTIONf_plane_restr0.00910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7912-2.25670.35851670.32781497X-RAY DIFFRACTION100
2.2567-30.25350.22941770.20151594X-RAY DIFFRACTION99
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)
10.00490.02390.03590.12410.23820.3741.04020.8972-2.40710.2914-0.0863-0.38760.42240.37140.05990.43410.0451-0.17330.4459-0.02020.695716.860912.560937.8684
20.3732-0.42040.0530.4153-0.04010.10890.15990.1325-0.6633-0.8474-0.51140.2454-0.2596-0.17420.00060.54520.0498-0.03260.4589-0.08770.42468.371211.844624.1912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )A1 - 5
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 10 )A6 - 10

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