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- PDB-3fl6: Influence of the incorporation of a cyclohexenyl nucleic acid (Ce... -

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Basic information

Entry
Database: PDB / ID: 3fl6
TitleInfluence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(GCGTGCG)/d(CGCACGC)
Components
  • 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3'
KeywordsDNA / double helix / CeNA / sugar modification / right-handed
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.17 Å
AuthorsRobeyns, K. / Herdewijn, P. / Van Meervelt, L.
Citation
Journal: Artif DNA PNA XNA / Year: 2010
Title: Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA.
Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L.
#1: Journal: Nucleic Acids Res. / Year: 2008
Title: Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG).
Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L.
#2: Journal: J.Am.Chem.Soc. / Year: 2008
Title: Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC.
Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jun 6, 2018Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3'
D: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,62411
Polymers8,4964
Non-polymers1,1287
Water2,342130
1
A: 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7315
Polymers4,2482
Non-polymers4833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3'
D: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8926
Polymers4,2482
Non-polymers6444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.720, 33.570, 81.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 2164.460 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'


Mass: 2083.388 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 289 K / pH: 5.5
Details: 10%(v/v) 2-methyl-2,4-pentanediol (MPD), 20mM cobalt hexamine, 40mM potassium cacodylate buffered at pH=5.5, and 80/12mM KCl/NaCl, vapor diffusion, hanging drop, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2cobalt hexamine11
3potassium cacodylate11
4KCl/NaCl11
5MPD12
6cobalt hexamine12
7potassium cacodylate12
8KCl/NaCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.7749
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2008
RadiationMonochromator: UNDULATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionRedundancy: 8.8 % / Av σ(I) over netI: 2.1 / Number: 71625 / Rmerge(I) obs: 0.16 / Rsym value: 0.16 / D res high: 1.7 Å / D res low: 19.858 Å / Num. obs: 8126 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.3819.8697.910.0990.0997.6
3.85.3899.410.1120.1128.6
3.13.89910.1260.1268.9
2.693.199.910.1310.1319.4
2.42.6999.510.1580.1589.2
2.192.499.210.2110.2119.3
2.032.1999.910.2570.2578.9
1.92.0399.210.3130.3138.9
1.791.999.710.3880.3888.8
1.71.7990.810.450.457.9
ReflectionResolution: 1.17→19.86 Å / Num. obs: 24411 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 3.735
Reflection shellResolution: 1.17→1.23 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.52 / % possible all: 98.8

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
125.04920.78817.51S201
229.94328.0210.886S200.902
316.75328.10125.184S200.718
413.92827.32336.351S200.487
516.52134.72332.23S200.47
620.91730.00717.408S200.304
734.24123.51918.922S200.246
87.86522.93339.072S200.228
914.70822.92727.468S200.212
1011.62833.00732.299S200.208
1115.03417.34331.396S200.203
1223.47825.9417.579S200.202
1323.08629.20927.464S200.197
1431.10624.61513.289S200.194
1516.87135.51716.773S200.191
1618.51434.36937.706S200.181
1726.37420.2844.129S200.178
1831.30228.77328.094S200.164
1917.1333.83523.168S200.163
208.27526.30343.335S200.161
2126.94933.4257.683S200.16
2222.65116.46715.283S200.159
2313.95726.74643.186S200.157
2433.828.3394.104S200.143
2512.19420.5436.346S200.139
2629.51622.54926.362S200.137
2715.30927.56312.601S200.128
2831.58933.920.824S200.125
2923.05332.93712.777S200.124
3029.38638.3849.018S200.123
3121.05935.0626.798S200.115
3216.23526.62531.519S200.095
3337.69428.21120.906S200.081
3416.26629.373.767S200.006

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
SHELXphasing
SHELXmodel building
SHELXrefinement
PDB_EXTRACT3.006data extraction
SHELXDphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.17→19.86 Å / Num. parameters: 6402 / Num. restraintsaints: 9922 / Occupancy max: 1 / Occupancy min: 0.22 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4%
RfactorNum. reflection% reflectionSelection details
all0.159 24372 --
obs0.145 20137 99.5 %-
Rfree-1221 -RANDOM
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 10.739 Å2
Refinement stepCycle: LAST / Resolution: 1.17→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 564 45 130 739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist0.002
X-RAY DIFFRACTIONs_from_restr_planes0.003
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr21
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps0.03
LS refinement shellResolution: 1.17→1.22 Å /
Rfactor% reflection
Rwork0.194 -
obs-98.71 %

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