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- PDB-250d: STRUCTURAL COMPARISON BETWEEN THE D(CTAG) SEQUENCE IN OLIGONUCLEO... -

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Basic information

Entry
Database: PDB / ID: 250d
TitleSTRUCTURAL COMPARISON BETWEEN THE D(CTAG) SEQUENCE IN OLIGONUCLEOTIDES AND TRP AND MET REPRESSOR-OPERATOR COMPLEXES
ComponentsDNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.47 Å
AuthorsUrpi, L. / Tereshko, V. / Malinina, L. / Huynh-Dinh, T. / Subirana, J.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met repressor-operator complexes.
Authors: Urpi, L. / Tereshko, V. / Malinina, L. / Huynh-Dinh, T. / Subirana, J.A.
#1: Journal: Biochemistry / Year: 1996
Title: Structure of the B-DNA Oligomers d(CGCTAGCG) and d(CGCTCTAGAGCG) in New Crystal Forms
Authors: Tereshko, R.V. / Urpi, L. / Malinina, L. / Huynh-Dinh, T. / Subirana, J.A.
History
DepositionFeb 22, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 19, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*CP*TP*AP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)14,5666
Polymers14,5666
Non-polymers00
Water61334
1
A: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.770, 41.520, 115.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.45836, -0.88836, -0.02688), (0.88845, 0.45879, -0.01269), (0.02361, -0.01807, 0.99956)-2.7013, 4.8829, 19.0474
2given(-0.54652, -0.83715, -0.02252), (0.83734, -0.54668, 0.00128), (-0.01338, -0.01816, 0.99975)-8.8749, 5.2194, 38.4659

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Components

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


Mass: 2427.605 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growMethod: vapor diffusion / pH: 6.2 / Details: pH 6.20, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 6.2
Components of the solutions
*PLUS
IDCommon nameCrystal-IDChemical formula
11Mg++
2spermine chloride1
31
41
51
61

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Data collection

DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.47 Å / Num. obs: 3742 / % possible obs: 80.6 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 2.47 Å / % possible obs: 80.6 %

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Processing

Software
NameClassification
X-PLORrefinement
MARXDSdata reduction
RefinementResolution: 2.47→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.182 --
obs0.182 3309 75.2 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.47→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1086 0 102 1188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.67
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.47 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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