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- PDB-1qp5: BASE-PAIRING SHIFT IN A DODECAMER CONTAINING A (CA)N TRACT -

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Basic information

Entry
Database: PDB / ID: 1qp5
TitleBASE-PAIRING SHIFT IN A DODECAMER CONTAINING A (CA)N TRACT
Components
  • DNA (5'-D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3')
KeywordsDNA / DNA-DNA INTERACTION / DNA SELF-FITTING / BASE PAIR SHIFT / FRAMESHIFT MUTATION / MICROSATELLITE INSTABILITY
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.6 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
DepositionJun 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP*A)-3')
B: DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,52210
Polymers7,3282
Non-polymers1948
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.900, 65.900, 47.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-75-

MG

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Components

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


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3')


Mass: 3710.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: WATER, SPERMINE, CACODYLATE, MAGNESIUM ACETATE, pH 6.0, VAPOR DIFFUSION at 277 K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE11
2CACODYLATECacodylic acid12
3MAGNESIUM ACETATE13
Crystal grow
*PLUS
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

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Data collection

DiffractionMean temperature: 258 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. all: 3519 / Num. obs: 1603 / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
ULTIMAmodel building
NUCLSQrefinement
X-GENdata reduction
X-GENdata scaling
ULTIMAphasing
RefinementResolution: 2.6→15 Å / σ(F): 2 / σ(I): 1 /
RfactorNum. reflection
all0.161 3519
obs0.161 1603
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 8 107 601
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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