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- PDB-1ikk: Intrinsic Bending and Deformability at the T-A step of CCTTTAAAGG... -

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Entry
Database: PDB / ID: 1ikk
TitleIntrinsic Bending and Deformability at the T-A step of CCTTTAAAGG: A Comparative Analysis of T-A and A-T steps within A-tracts
Components5'-D(*CP*CP*TP*TP*TP*AP*AP*AP*GP*G)-3'
KeywordsDNA / B-DNA double helix / A-tract containing a T-A step
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMack, D.R. / Chiu, T.K. / Dickerson, R.E.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts.
Authors: Mack, D.R. / Chiu, T.K. / Dickerson, R.E.
History
DepositionMay 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: 5'-D(*CP*CP*TP*TP*TP*AP*AP*AP*GP*G)-3'
B: 5'-D(*CP*CP*TP*TP*TP*AP*AP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1856
Polymers6,0882
Non-polymers974
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.558, 38.737, 32.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3044.016 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: It was synthesized on a Eppendorf ECOSYN D300 Synthesizer
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.84 Å3/Da / Density % sol: 33.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Spermine-HCL, Mg(OAc)2, MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Spermine-HCl11
2Mg(OAc)211
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.86 mMprotein1drop
20.35 mMspermine hydrochloride1drop
35.00 mMmagnesium acetate1drop
412.5 %(v/v)1drop
520 %MPD1reservoir

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Data collection

DiffractionMean temperature: 116 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 6276 / Num. obs: 6263 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 26.2
Reflection shellResolution: 1.6→1.72 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 11.2 / % possible all: 98
Reflection
*PLUS
Num. measured all: 65685
Reflection shell
*PLUS
% possible obs: 98 % / Mean I/σ(I) obs: 11.17

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB entry bdj036

Resolution: 1.6→40 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2
RfactorNum. reflectionSelection details
Rfree0.236 627 random
Rwork0.177 --
all0.192 6236 -
obs0.184 5756 -
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 28 109 541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d2.32
X-RAY DIFFRACTIONs_bond_d0.013
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 4 / Rfactor obs: 0.1794 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 2.32
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.72 Å / Rfactor Rfree: 0.3228 / Rfactor obs: 0.2518

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