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- PDB-206d: BASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED I... -

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Basic information

Entry
Database: PDB / ID: 206d
TitleBASE-PAIR OPENING AND SPERMINE BINDING-B-DNA FEATURES DISPLAYED IN THE CRYSTAL STRUCTURE OF A GAL OPERON FRAGMENT: IMPLICATIONS FOR PROTEIN-DNA RECOGNITION
Components
  • DNA (5'-D(*CP*CP*AP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsTari, L.W. / Secco, A.S.
CitationJournal: Nucleic Acids Res. / Year: 1995
Title: Base-pair opening and spermine binding--B-DNA features displayed in the crystal structure of a gal operon fragment: implications for protein-DNA recognition.
Authors: Tari, L.W. / Secco, A.S.
History
DepositionApr 19, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 21, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*GP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0244
Polymers3,6192
Non-polymers4052
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.450, 54.450, 42.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-28-

HOH

21A-29-

HOH

31A-30-

HOH

41A-31-

HOH

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Components

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


Mass: 1865.240 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*CP*AP*CP*CP*G)-3')


Mass: 1754.182 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMDNA duplex1drop
210 mM1dropMgCl2
35 mMspermine1drop
430 mMsodium cacodylate1drop
510 %(v/v)MPD1drop
625 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 277 K
DetectorType: RIGAKU AFC-6S / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 1233 / Observed criterion σ(F): 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→20 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.221 -
obs0.221 392
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTFisotropic
ALL WATERSX-RAY DIFFRACTIONTFisotropic
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 272 21 17 310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.029
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_deg5.2
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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