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- PDB-455d: A6/A18 INTER-STRAND DITHIOBIS(PROPANE)-CROSSLINKED DODECAMER (CGC... -

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Basic information

Entry
Database: PDB / ID: 455d
TitleA6/A18 INTER-STRAND DITHIOBIS(PROPANE)-CROSSLINKED DODECAMER (CGCGAATTCGCG)2
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*(SSP)AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / INTER-STRAND CROSSLINKING / DODECAMER CGCGAATTCGCG/CGCGAATTCGCG / DEOXYRIBONUCLEIC ACID
Function / homologyDITHIOBIS-(PROPANE) / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 1.43 Å
AuthorsChiu, T.K. / Kaczor-Grzeskowiak, M. / Dickerson, R.E.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G.
Authors: Chiu, T.K. / Kaczor-Grzeskowiak, M. / Dickerson, R.E.
History
DepositionMar 4, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2019Group: Advisory / Data collection / Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / struct_conn
Item: _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.inclination
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,5506
Polymers7,3272
Non-polymers2234
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.544, 39.303, 66.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COMPLEXED WITH THIOPROPANE
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SSP / DITHIOBIS-(PROPANE)


Mass: 150.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.78 Å3/Da / Density % sol: 30.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2SPERMINE11
3DITHIOTHREITOL11
4MPD11
5MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMdodecamer1drop
220 mM1dropMgCl2
30.6 mMspermine hydrochloride1drop
420 mMdithiothreitol1drop
54.6 %(v/v)1drop
635 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.43→8 Å / Num. obs: 11200 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 9.49 % / Biso Wilson estimate: 17.85 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 38.1
Reflection shellResolution: 1.43→1.54 Å / Redundancy: 6.73 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 10.9 / % possible all: 80.8
Reflection
*PLUS
Lowest resolution: 8 Å / Observed criterion σ(I): 2 / Num. measured all: 106309
Reflection shell
*PLUS
% possible obs: 80.8 % / Mean I/σ(I) obs: 10.93

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMEN
Starting model: IDEAL B-DNA

Resolution: 1.43→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: STARTING MODEL IS IDEAL B-DNA RMS-FITTED ONTO COORDINATES OF ORIGINAL DREW STRUCTURE (1BNA)
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1055 10 %RANDOM
Rwork0.208 ---
obs0.208 11016 88.5 %-
Displacement parametersBiso mean: 13.56 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å20 Å2
2---3.12 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.43→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 28 133 647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.65
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.65
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

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