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

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Basic information

Entry
Database: PDB / ID: 5fhj
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 / amphimorphism / double-folded / B-type helix
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,59311
Polymers12,1804
Non-polymers4137
Water1,53185
1
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
B: DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3857
Polymers6,0902
Non-polymers2955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2084
Polymers6,0902
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.500, 48.500, 111.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

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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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.62 Å3/Da / Density % sol: 53.2 % / Description: tetragonal prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 50 mM sodium cacodylate buffer, 10 mM cobalt chloride, 0.5 mM spermine, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.605, 0.976
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2013 / Details: Bent collimating mirror
RadiationMonochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.6051
20.9761
ReflectionResolution: 1.68→29.44 Å / Num. obs: 15873 / % possible obs: 99.9 % / Redundancy: 28 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.8
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 25.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MxCuBE2data collection
MOSFLM7.0.9data processing
PHENIX1.9_1692phasing
MOSFLM7.0.9data reduction
Aimless0.2.17data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.68→29.437 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.5 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 2786 9.87 %Random selection
Rwork0.209 ---
obs0.2107 15873 97.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→29.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 7 85 900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004904
X-RAY DIFFRACTIONf_angle_d0.6241388
X-RAY DIFFRACTIONf_dihedral_angle_d34.555384
X-RAY DIFFRACTIONf_chiral_restr0.032156
X-RAY DIFFRACTIONf_plane_restr0.00340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.7090.27411280.2591236X-RAY DIFFRACTION95
1.709-1.740.2471320.2241244X-RAY DIFFRACTION94
1.74-1.77350.27841230.24341209X-RAY DIFFRACTION94
1.7735-1.80970.30631330.21851267X-RAY DIFFRACTION96
1.8097-1.8490.28361370.23651268X-RAY DIFFRACTION96
1.849-1.8920.27211360.23831230X-RAY DIFFRACTION95
1.892-1.93930.26991380.24261238X-RAY DIFFRACTION95
1.9393-1.99180.27591410.24121272X-RAY DIFFRACTION98
1.9918-2.05040.23171420.21291281X-RAY DIFFRACTION99
2.0504-2.11650.23191450.22331284X-RAY DIFFRACTION99
2.1165-2.19210.22621370.21421273X-RAY DIFFRACTION99
2.1921-2.27990.23961430.21071302X-RAY DIFFRACTION99
2.2799-2.38360.21581420.21481283X-RAY DIFFRACTION99
2.3836-2.50920.23021430.22551294X-RAY DIFFRACTION100
2.5092-2.66630.25161490.23961285X-RAY DIFFRACTION100
2.6663-2.8720.24271420.23521315X-RAY DIFFRACTION100
2.872-3.16080.23161400.2291284X-RAY DIFFRACTION100
3.1608-3.61740.2261470.21011302X-RAY DIFFRACTION99
3.6174-4.55480.19551450.18031287X-RAY DIFFRACTION100
4.5548-29.44160.19761430.16571275X-RAY DIFFRACTION98

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