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- PDB-1d26: EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFOR... -

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Basic information

Entry
Database: PDB / ID: 1d26
TitleEFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX
ComponentsDNA (5'-D(*GP*CP*CP*CP*(G31)P*GP*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.12 Å
AuthorsHeinemann, U.
Citation
Journal: Nucleic Acids Res. / Year: 1991
Title: Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix.
Authors: Heinemann, U. / Rudolph, L.N. / Alings, C. / Morr, M. / Heikens, W. / Frank, R. / Blocker, H.
#1: Journal: Structure and Methods. DNA and RNA / Year: 1990
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.
#3: Journal: Nucleosides and Nucleotides / Year: 1988
Title: X-Ray Crystallographic Studies of the A-Form of DNA
Authors: Heinemann, U. / Lauble, H. / Frank, R. / Bloecker, H.
#4: Journal: Nucleic Acids Res. / Year: 1987
Title: Crystal Structure Analysis of an A-DNA Fragment at 1.8 Angstroms Resolution: d(GCCCGGGC)
Authors: Heinemann, U. / Lauble, H. / Frank, R. / Bloecker, H.
History
DepositionSep 17, 1990Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 7, 1992Provider: 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 / diffrn_source / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*CP*CP*(G31)P*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4271
Polymers2,4271
Non-polymers00
Water52229
1
A: DNA (5'-D(*GP*CP*CP*CP*(G31)P*GP*GP*C)-3')

A: DNA (5'-D(*GP*CP*CP*CP*(G31)P*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)43.300, 43.300, 24.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*GP*CP*CP*CP*(G31)P*GP*GP*C)-3')


Mass: 2426.620 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7 / Details: pH 7.00, MICRODIALYSIS, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3BIS-TRIS-PROPANE_HCL11
4MG ACETATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetailsSol-ID
18.3 mMDNA1single strand
210 mMTris-HCl1
310 mMmagnesium acetate1
45 %(v/v)MPD12
510 mMTris-HCl1
610 mMmagnesium acetate1

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31
DetectorType: ARNDT-WONACOTT / Detector: OSCILLATION CAMERA
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.12→6 Å / Num. obs: 1303 / Observed criterion σ(F): 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.12→6 Å / σ(F): 3 /
RfactorNum. reflection
obs0.16 1197
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.12→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 160 1 29 190
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_it3.135
X-RAY DIFFRACTIONn_sugar_angle_it3.926.5
X-RAY DIFFRACTIONn_phos_bond_it4.817.5
X-RAY DIFFRACTIONn_phos_angle_it4.377.5
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0150.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0350.05
X-RAY DIFFRACTIONn_phos_bond_d0.0550.05
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0740.075
X-RAY DIFFRACTIONn_plane_restr0.020.03
X-RAY DIFFRACTIONn_chiral_restr0.0720.1
X-RAY DIFFRACTIONn_singtor_nbd0.1320.25
X-RAY DIFFRACTIONn_multtor_nbd0.2080.25
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.12 Å / Lowest resolution: 6 Å / Num. reflection obs: 1197 / σ(I): 3 / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.015
X-RAY DIFFRACTIONn_angle_d0.0350.05

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