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- PDB-1bd1: CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA -

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Basic information

Entry
Database: PDB / ID: 1bd1
TitleCRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA
ComponentsDNA (5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyTRIETHYLAMMONIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsHeinemann, U.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Crystallographic study of one turn of G/C-rich B-DNA.
Authors: Heinemann, U. / Alings, C.
#1: Journal: Structure and Methods. DNA and RNA / Year: 1989
Title: Structural Features of G/C-Rich DNA Going A or B
Authors: Heinemann, U. / Alings, C. / Lauble, H.
#2: Journal: Nucleosides and Nucleotides / Year: 1990
Title: X-Ray Studies of DNA Aiming at Elucidating the Sequence-Structure Code
Authors: Heinemann, U. / Alings, C. / Lauble, H.
History
DepositionAug 16, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,2503
Polymers3,0461
Non-polymers2042
Water73941
1
A: DNA (5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,5016
Polymers6,0922
Non-polymers4094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)32.150, 25.490, 34.820
Angle α, β, γ (deg.)90.00, 116.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-40-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-TEA / TRIETHYLAMMONIUM ION


Mass: 102.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 277 K / Method: microdialysis / Details: MICRODIALYSIS, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2ISOPROPANOL OR MPD11
3BIS-TRIS-PROPANE_HCL11
4MGCL211
5ISOPROPANOL OR MPD11

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: SEALED TUBE
DetectorDetector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.4 Å / Num. obs: 3062
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.6 Å / Rmerge(I) obs: 0.038

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.6→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.16 2106
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
TWO (C2H5)3NH+X-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 10 41 253
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it3.435
X-RAY DIFFRACTIONn_sugar_angle_it4.397.5
X-RAY DIFFRACTIONn_phos_bond_it3.757.5
X-RAY DIFFRACTIONn_phos_angle_it3.627.5
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0140.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0430.05
X-RAY DIFFRACTIONn_phos_bond_d0.050.05
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0730.075
X-RAY DIFFRACTIONn_plane_restr0.0250.03
X-RAY DIFFRACTIONn_chiral_restr0.0660.1
X-RAY DIFFRACTIONn_singtor_nbd0.1280.25
X-RAY DIFFRACTIONn_multtor_nbd0.2320.25
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 3 / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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