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- PDB-436d: THE DICKERSON-DREW B-DNA DODECAMER REVISITED-AT ATOMIC RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 436d
TitleTHE DICKERSON-DREW B-DNA DODECAMER REVISITED-AT ATOMIC RESOLUTION
Components5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3'
KeywordsDNA / B-DNA DODECAMER / HIGH RESOLUTION
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsTereshko, V. / Minasov, G. / Egli, M.
CitationJournal: J.Am.Chem.Soc. / Year: 1999
Title: The Dickerson-Drew B-DNA Dodecamer Revisited-At Atomic Resolution
Authors: Tereshko, V. / Minasov, G. / Egli, M.
History
DepositionNov 12, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,4847
Polymers7,3632
Non-polymers1225
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.640, 39.630, 65.530
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 5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3'


Mass: 3681.383 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: SODIUM CACODYLATE, MAGNESIUM ACETATE, SPERMINE; PRECIPITANT: MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MAGNESIUM ACETATE11
3SPERMINE11
4MPD12
Crystal grow
*PLUS
pH: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mMDNA1drop
220 mMsodium cacodylate1drop
325 mM1dropMg(OAc)2
43 mMspermine 4HCl1drop
540 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 1998
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. all: 26878 / Num. obs: 26878 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.066
Reflection shellResolution: 1.1→1.2 Å / Rmerge(I) obs: 0.154 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 1.1 Å
Reflection shell
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 1.2 Å / % possible obs: 99.7 % / Num. unique obs: 6060 / Mean I/σ(I) obs: 8.5

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.1→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
all0.162 26721 -
obs0.162 26721 99.6 %
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 7 231 724
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 0.02
LS refinement shell
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 1.2 Å / Rfactor obs: 0.22

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