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- PDB-2qef: X-ray structure of 7-deaza-dG and Z3dU modified duplex CGCGAATXCZCG -

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Basic information

Entry
Database: PDB / ID: 2qef
TitleX-ray structure of 7-deaza-dG and Z3dU modified duplex CGCGAATXCZCG
ComponentsDNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*(ZDU)P*DCP*(7GU)P*DCP*DG)-3')
KeywordsDNA / B-DNA / Z3dU / 7-deaza-dG
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, F. / Li, F. / Ganguly, M. / Marky, L.A. / Gold, B. / Egli, M. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2008
Title: A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' ...Title: A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards.
Authors: Wang, F. / Li, F. / Ganguly, M. / Marky, L.A. / Gold, B. / Egli, M. / Stone, M.P.
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 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 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*(ZDU)P*DCP*(7GU)P*DCP*DG)-3')
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*(ZDU)P*DCP*(7GU)P*DCP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)7,4112
Polymers7,4112
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint21.5 kcal/mol
Surface area4130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.858, 41.057, 66.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*(ZDU)P*DCP*(7GU)P*DCP*DG)-3')


Mass: 3705.472 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The oligodeoxynucleotide 5'-d(CGCGAATXCZCG)-3' (DDD2+/Z10) was synthesized and purified using reversed-phase semipreparative HPLC (Phenomenex, Phenyl-Hexyl, 5 m, 250 10.0 mm) equilibrated ...Details: The oligodeoxynucleotide 5'-d(CGCGAATXCZCG)-3' (DDD2+/Z10) was synthesized and purified using reversed-phase semipreparative HPLC (Phenomenex, Phenyl-Hexyl, 5 m, 250 10.0 mm) equilibrated with 0.1 M ammonium formate (pH 7.0) and desalted using G25 column.
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Final droplets contain 0.6 mM oligonucleotides, 5% MPD, 20 mM sodium cacodylate, 6 mM spermine tetrahydrochloride, 40 mM KCl and 10 mM MgCl2., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3spermine tetrahydrochloride11
4KCl11
5MgCl211
6MPD12
7sodium cacodylate12
8spermine tetrahydrochloride12
9KCl12
10MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→34.94 Å / Num. all: 9574 / Num. obs: 8368 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.133 / Num. unique all: 821 / % possible all: 62.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 355D

355d


Resolution: 1.6→34.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.317 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.134 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23114 497 5.6 %RANDOM
Rwork0.18112 ---
all0.18365 9574 --
obs0.18112 8368 93.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.313 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 492 0 96 588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021546
X-RAY DIFFRACTIONr_bond_other_d0.0020.02238
X-RAY DIFFRACTIONr_angle_refined_deg1.5963822
X-RAY DIFFRACTIONr_angle_other_deg1.0963596
X-RAY DIFFRACTIONr_chiral_restr0.0640.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.02248
X-RAY DIFFRACTIONr_nbd_refined0.5260.276
X-RAY DIFFRACTIONr_nbd_other0.2510.2261
X-RAY DIFFRACTIONr_nbtor_refined0.2490.2189
X-RAY DIFFRACTIONr_nbtor_other0.0810.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0080.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1360.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.25
X-RAY DIFFRACTIONr_scbond_it3.7353786
X-RAY DIFFRACTIONr_scangle_it4.8934.5822
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 24 -
Rwork0.162 336 -
obs--52.94 %
Refinement TLS params.Method: refined / Origin x: 14.8814 Å / Origin y: 20.6298 Å / Origin z: 9.3648 Å
111213212223313233
T0.0089 Å20.0145 Å20.0131 Å2-0.0206 Å20.0115 Å2--0.0072 Å2
L0.0843 °20.0026 °2-0.016 °2-0.0169 °20.1719 °2--1.7745 °2
S0.0514 Å °-0.0148 Å °0.009 Å °-0.006 Å °0.0436 Å °-0.0145 Å °0.0261 Å °-0.0591 Å °-0.095 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 121 - 12
2X-RAY DIFFRACTION1BB1 - 121 - 12

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