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- PDB-2oks: X-ray Structure of a DNA Repair Substrate Containing an Alkyl Int... -

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Entry
Database: PDB / ID: 2oks
TitleX-ray Structure of a DNA Repair Substrate Containing an Alkyl Interstrand Crosslink at 1.65 Resolution
Components5'-D(*CP*CP*AP*AP*(C34)P*GP*TP*TP*GP*G)-3'
KeywordsDNA / INTERSTRAND CROSSLINK / DNA DAMAGE
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsSwenson, M.C. / Paranawithana, S.R. / Miller, P.S. / Kielkopf, C.L.
CitationJournal: Biochemistry / Year: 2007
Title: Structure of a DNA repair substrate containing an alkyl interstrand cross-link at 1.65 a resolution.
Authors: Swenson, M.C. / Paranawithana, S.R. / Miller, P.S. / Kielkopf, C.L.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 30, 2014Group: Non-polymer description / Structure summary
Revision 1.4Jan 11, 2017Group: Other
Revision 1.5Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THIS IS A N4C-ETHYL-N4C CROSSLINKED DNA. ONLY HALF OF THE ETHYL LINKER IS PRESENT IN THE ...HETEROGEN THIS IS A N4C-ETHYL-N4C CROSSLINKED DNA. ONLY HALF OF THE ETHYL LINKER IS PRESENT IN THE COORDINATES SINCE IT IS LOCATED ON THE TWO-FOLD AXES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*AP*AP*(C34)P*GP*TP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1794
Polymers3,0591
Non-polymers1203
Water1,35175
1
A: 5'-D(*CP*CP*AP*AP*(C34)P*GP*TP*TP*GP*G)-3'
hetero molecules

A: 5'-D(*CP*CP*AP*AP*(C34)P*GP*TP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3598
Polymers6,1182
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)31.870, 24.890, 34.350
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a double-stranded DNA generated by the crystallographic two-fold axis

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Components

#1: DNA chain 5'-D(*CP*CP*AP*AP*(C34)P*GP*TP*TP*GP*G)-3'


Mass: 3059.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid phase synthesis of DNA oligo, crosslink phosphoramidite synthesized separately
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growpH: 8
Details: The purified crosslinked DNA was dissolved in a buffer containing 22 mM ammonium acetate, 11 mM tris-hydroxymethyl-aminomethane (Tris)-HCl pH 8.0, and 11 mM calcium acetate. Crystals were ...Details: The purified crosslinked DNA was dissolved in a buffer containing 22 mM ammonium acetate, 11 mM tris-hydroxymethyl-aminomethane (Tris)-HCl pH 8.0, and 11 mM calcium acetate. Crystals were grown using the sitting drop vapor diffusion method at 277K, in which 3 uL of a reservoir solution containing 27% 2-3 methyl-pentadiol, 115 mM calcium acetate, and 10 mM Tris-HCl pH 8.0 was added to an equal volume of DNA solution, and the mixture was equilibrated against 700 uL of the reservoir solution. Crystals first appeared after two weeks.
Components of the solutions
IDNameCrystal-IDSol-ID
12-3 methyl-pentadiol11
2calcium acetate11
3Tris-HCl11
4ammonium acetate11
5H2O11
62-3 methyl-pentadiol12
7calcium acetate12
8Tris-HCl12
9H2O12

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2004
RadiationMonochromator: mirrors, graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 3043 / Num. obs: 2924 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 8 Å2 / Rsym value: 0.046 / Net I/σ(I): 38.1
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.56 % / Mean I/σ(I) obs: 25.7 / Num. unique all: 239 / Rsym value: 0.047 / % possible all: 79.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1EN8

1en8


Resolution: 1.65→18.89 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 992530.75 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic individual / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.208 162 5.5 %RANDOM
Rwork0.182 ---
all-3043 --
obs-2924 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.6312 Å2 / ksol: 0.353499 e/Å3
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20.75 Å2
2--0.62 Å20 Å2
3---0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.15 Å
Refinement stepCycle: LAST / Resolution: 1.65→18.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 203 3 75 281
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d2.14
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 27 6.3 %
Rwork0.24 403 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1xlink2.paramxlink2.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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