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- PDB-330d: BASE-PAIRING SHIFT IN THE MAJOR GROOVE OF (CA)N TRACTS BY B-DNA C... -

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Basic information

Entry
Database: PDB / ID: 330d
TitleBASE-PAIRING SHIFT IN THE MAJOR GROOVE OF (CA)N TRACTS BY B-DNA CRYSTAL STRUCTURES
Components
  • DNA (5'-D(*AP*CP*CP*GP*CP*CP*GP*GP*CP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*GP*CP*CP*GP*GP*CP*GP*GP*T)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTimsit, Y. / Vilbois, E. / Moras, D.
Citation
Journal: Nature / Year: 1991
Title: Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures.
Authors: Timsit, Y. / Vilbois, E. / Moras, D.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Self-fitting and Self-modifying Properties of the B-DNA Molecule
Authors: Timsit, Y. / Moras, D.
History
DepositionApr 29, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 30, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*GP*CP*CP*GP*GP*CP*GP*CP*C)-3')
B: DNA (5'-D(*GP*GP*CP*GP*CP*CP*GP*GP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,3302
Polymers7,3302
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.890, 65.890, 47.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 3609.345 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*CP*GP*CP*CP*GP*GP*CP*GP*GP*T)-3')


Mass: 3720.403 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CACODYLATE11
4SPERMINE11
5MG ACETATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMcacodylate1drop
21 mMdodecamer duplex1drop
31.2 mMspermine tetrachloride1drop
416 mMmagnesium acetate1drop
545 %2,4-methypentanediol1drop
61
71

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Data collection

DiffractionMean temperature: 258 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 1710 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
X-PLORrefinement
CORELSrefinement
ULTIMAmodel building
XENGENdata reduction
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B-DNA DODECAMER

Resolution: 2.7→7 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 0.001 / σ(F): 2
Details: RE-REFINEMENT OF THE PUBLISHED STRUCTURE WITH NEW VERSION OF TOPOLOGY AND PARAMETERS FILES (1996), AND NEW VERSION OF X-PLOR (1997).
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 1378 69.7 %
Displacement parametersBiso mean: 34 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 52 538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.27
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.83
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA.PARAMDNA.TOP
X-RAY DIFFRACTION2PARAM19.SOLTOPH10.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 7 Å / σ(F): 2 / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.83

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