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- PDB-3lln: Comparison between the orthorhombic an tetragonal form of the hep... -

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Basic information

Entry
Database: PDB / ID: 3lln
TitleComparison between the orthorhombic an tetragonal form of the heptamer sequence d(GCG(xT)GCG)/d(CGCACGC).
Components
  • DNA (5'-D(*CP*GP*CP*AP*CP*GP*C)-3')
  • DNA (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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRobeyns, K. / Herdewijn, P. / Van Meervelt, L.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Comparison between the orthorhombic and tetragonal forms of the heptamer sequence d[GCG(xT)GCG]/d(CGCACGC)
Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L.
#1: 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.
#2: 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.
#3: Journal: Artificial DNA / Year: 2010
Title: Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA
Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4093
Polymers4,2482
Non-polymers1611
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-3 kcal/mol
Surface area3020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.482, 25.482, 81.147
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
11B-4-

HOH

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Components

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


Mass: 2164.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED ON SOLID SUPPORT
#2: DNA chain DNA (5'-D(*CP*GP*CP*AP*CP*GP*C)-3')


Mass: 2083.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED ON SOLID SUPPORT
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2007 / Details: mirror
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→18.55 Å / Num. all: 681 / Num. obs: 681 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 4.5 / Num. unique all: 93 / Rsym value: 0.174 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FL6 (one biological unit)

3fl6


Resolution: 3→18.15 Å / Cor.coef. Fo:Fc: 0.96 / SU B: 14.93 / SU ML: 0.291 / Isotropic thermal model: ISOTROPIC / Cross valid method: NONE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rwork0.22599 ---
all0.22599 678 --
obs0.22599 678 98.55 %-
Rfree---NONE
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 71.704 Å2
Baniso -1Baniso -2Baniso -3
1-6.73 Å20 Å20 Å2
2--6.73 Å20 Å2
3----13.45 Å2
Refinement stepCycle: LAST / Resolution: 3→18.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 282 7 9 298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9432.922607
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.1220.253
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02151
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it2.1033321
X-RAY DIFFRACTIONr_scangle_it3.2294.5497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.001→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.195 41 -
obs-678 100 %

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