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- PDB-2p8d: The Structure of the Dickerson Sequence with an Incorporated CeNA... -

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Basic information

Entry
Database: PDB / ID: 2p8d
TitleThe Structure of the Dickerson Sequence with an Incorporated CeNA Residue
Components5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3'
KeywordsDNA / CeNA / sugar modification
Function / homologyCOBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRobeyns, K. / Van Meervelt, L.
CitationJournal: 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.
History
DepositionMar 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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: 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3'
B: 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8305
Polymers7,3472
Non-polymers4833
Water1,33374
1
A: 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3'

A: 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3'


Theoretical massNumber of molelcules
Total (without water)7,3472
Polymers7,3472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area2410 Å2
ΔGint2.9 kcal/mol
Surface area4230 Å2
MethodPISA
2
B: 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3'
hetero molecules

B: 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3148
Polymers7,3472
Non-polymers9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3310 Å2
ΔGint7.7 kcal/mol
Surface area4580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.915, 38.780, 66.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-13-

HOH

21A-35-

HOH

31B-107-

HOH

41B-147-

HOH

DetailsThe second part of the biological assembly of chain A is generated by the two fold axis: -x-1, y, -z-0.5 / The second part of the biological assembly of chain B is generated by the two fold axis: x, -y, -z

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Components

#1: DNA chain 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3'


Mass: 3673.430 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The XAR (Cyclohexene nucleic acid) residues as well as the oligomer sequence were synthesized.
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20mM potassium cacodylate buffer (pH=5.5), 10mM cobalt hexamine, 44mM potassium chloride, 6mM sodium chloride, 5%(v/v) 2-methyl-2,4-pentanediol (MPD), and 0.75mM ssDNA against a 35%(v/v) MPD ...Details: 20mM potassium cacodylate buffer (pH=5.5), 10mM cobalt hexamine, 44mM potassium chloride, 6mM sodium chloride, 5%(v/v) 2-methyl-2,4-pentanediol (MPD), and 0.75mM ssDNA against a 35%(v/v) MPD stock solution, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1potassium cacodylate11
2cobalt hexamine11
3potassium chloride11
4sodium chloride11
52-methyl-2,4-pentanediol (MPD)11
62-methyl-2,4-pentanediol (MPD)12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8414 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8414 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 5476 / Num. obs: 5476 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3 / Num. unique all: 777 / Rsym value: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 355D

355d


Resolution: 1.9→17.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.408 / SU ML: 0.148 / Isotropic thermal model: Idotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.194 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30752 245 4.5 %RANDOM
Rwork0.22954 ---
all0.23313 5209 --
obs0.23313 5209 99.27 %-
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: 44.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 469 21 74 564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.80331103
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_restr0.0870.288
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02247
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2149
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.2305
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.233
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_it2.0193787
X-RAY DIFFRACTIONr_scangle_it3.1494.5842
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 14 -
Rwork0.355 384 -
obs-777 100 %

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