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- PDB-249d: STRUCTURAL COMPARISON BETWEEN THE D(CTAG) SEQUENCE IN OLIGONUCLEO... -

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Basic information

Entry
Database: PDB / ID: 249d
TitleSTRUCTURAL COMPARISON BETWEEN THE D(CTAG) SEQUENCE IN OLIGONUCLEOTIDES AND TRP AND MET REPRESSOR-OPERATOR COMPLEXES
ComponentsDNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 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 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,6945
Polymers14,6544
Non-polymers401
Water84747
1
A: DNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3673
Polymers7,3272
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.050, 68.910, 26.150
Angle α, β, γ (deg.)90.00, 91.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3663.392 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CACL211
4WATER12
5MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDCrystal-IDChemical formula
11Ca++
21
31
41
51

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Data collection

DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Apr 3, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.25 Å / Num. obs: 5276 / % possible obs: 88.9 % / Rmerge(I) obs: 0.09
Reflection
*PLUS
Highest resolution: 2.25 Å / % possible obs: 88.9 % / Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
X-PLORrefinement
ENRAF-NONIUSdata reduction
RefinementResolution: 2.25→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.197 --
obs0.197 4222 72.4 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1048 1 141 1190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg4.1
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: 2.25 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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