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- PDB-355d: THE B-DNA DODECAMER AT HIGH RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 355d
TitleTHE B-DNA DODECAMER AT HIGH RESOLUTION
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / SODIUM FORM
Function / homologySPERMINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsHu, L.D. / Shui, X. / McFail-Isom, L. / Williams, G.G.
CitationJournal: Biochemistry / Year: 1998
Title: The B-DNA dodecamer at high resolution reveals a spine of water on sodium.
Authors: Shui, X. / McFail-Isom, L. / Hu, G.G. / Williams, L.D.
History
DepositionOct 7, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 13, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,5534
Polymers7,3272
Non-polymers2272
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.186, 40.208, 65.656
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(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6N,N'-BIS(4-AMINOBUTYL)-(2,7-ANTHROQUINONEDISULFONAMIDE DIHYDROCHLORIDE)11
7WATER12
8MPD12
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8 mMDNA1drop
231 mMsodium cacodylate1drop
39.6 mM1dropMgCl2
47 %MPD1drop
538 mMspermine tetrahydrochloride1drop
61.0 mMN,N'-BIS(4-AMINOBUTYL)-2,7-ANTHROQUINONEDISULFONAMIDE DIHYDROCHLORIDE1drop
730 %MPD1reservoir
81

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Data collection

DiffractionMean temperature: 136 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: ADSC / Detector: CCD
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.38 Å / Num. all: 58307 / Num. obs: 11594
Reflection
*PLUS
Highest resolution: 1.38 Å / Lowest resolution: 10 Å / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 1.38 Å / Lowest resolution: 1.48 Å / Rmerge(I) obs: 0.117

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Processing

Software
NameClassification
X-PLORrefinement
ADSCdata collection
RefinementStarting model: NDB ENTRY GDL036 (PDB ENTRY 227D)

227d


Resolution: 1.4→10 Å / σ(F): 0
RfactorNum. reflection
Rfree0.216 -
Rwork0.197 -
obs0.197 11438
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 14 160 660
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
LS refinement shellResolution: 1.4→1.46 Å
RfactorNum. reflection% reflection
Rwork0.241 784 -
obs--64 %
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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