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- PDB-1sk5: The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation... -

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Basic information

Entry
Database: PDB / ID: 1sk5
TitleThe ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition
Components5'-D(*CP*TP*TP*TP*TP*AP*AP*AP*AP*G)-3'
KeywordsDNA / DNA/DNA double helix / Popypurine Tract Sequence of HIV-1
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.89 Å
AuthorsHan, G.W. / Langs, D. / Kopka, M.L. / Dickerson, R.E.
Citation
Journal: To be Published
Title: The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition
Authors: Han, G.W. / Langs, D. / Kopka, M.L. / Dickerson, R.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Direct-methods determination of an RNA/DNA hybrid decamer at 1.15A Resolution
Authors: Han, G.W.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: An Unusual Sugar Conformation in the Structure of an RNA/DNA Decamer of the Polypurine Tract May Affect Recognition by Rnase H
Authors: Kopka, M.L. / Lavelle, L. / Han, G.W. / Ng, H.L. / Dickerson, R.E.
#3: Journal: J.Mol.Biol. / Year: 1997
Title: Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis
Authors: Han, G.W. / Kopka, M.L. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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_alt_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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: 5'-D(*CP*TP*TP*TP*TP*AP*AP*AP*AP*G)-3'
B: 5'-D(*CP*TP*TP*TP*TP*AP*AP*AP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,40710
Polymers6,0862
Non-polymers3218
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.665, 35.664, 28.289
Angle α, β, γ (deg.)90.00, 101.69, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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


Mass: 3043.028 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: SYNTHESIZED BY THE SOLID-PHASE PHOSPHORAMIDATE METHOD ON AN EPPENDORF ECOSYN D300 SYNTHESIZER
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 33.14 %
Crystal growMethod: vapor diffusion, hanging drop
Details: Calcium acetate, Spermine, MPD, VAPOR DIFFUSION, HANGING DROP, temperature 269K
Components of the solutions
IDNameCrystal-IDSol-ID
1Calcium acetate11
2Spermine11
3MPD11
4Calcium acetate12
5MPD12

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.89→50 Å / Num. all: 32054 / Num. obs: 32054 / Redundancy: 10.2 % / Rsym value: 0.073
Reflection shellResolution: 0.89→0.92 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.573

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SnBphasing
CROQUEmodel building
SHELXL-97refinement
CROQUEphasing
RefinementStarting model: NONE

Resolution: 0.89→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.144 1507 -RANDOM
Rwork0.1263 ---
obs0.12631 30438 5 %-
all-32054 --
Refinement stepCycle: LAST / Resolution: 0.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 422 55 110 587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.026
LS refinement shellResolution: 0.89→0.94 Å / Rfactor Rwork: 0.235

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