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- PDB-1cs7: SYNTHETIC DNA HAIRPIN WITH STILBENEDIETHER LINKER -

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Basic information

Entry
Database: PDB / ID: 1cs7
TitleSYNTHETIC DNA HAIRPIN WITH STILBENEDIETHER LINKER
Components5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
KeywordsDNA / DNA HAIRPIN
Function / homologySTRONTIUM ION / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLewis, F.D. / Liu, X. / Wu, Y. / Miller, S.E. / Wasielewski, M.R. / Letsinger, R.L. / Sanishvili, R. / Joachimiak, A. / Tereshko, V. / Egli, M.
CitationJournal: J.Am.Chem.Soc. / Year: 1999
Title: Structure and Photoinduced Electron Transfer in Exceptionally Stable Synthetic DNA Hairpins with Stilbenediether Linkers
Authors: Lewis, F.D. / Liu, X. / Wu, Y. / Miller, S.E. / Wasielewski, M.R. / Letsinger, R.L. / Sanishvili, R. / Joachimiak, A. / Tereshko, V. / Egli, M.
History
DepositionAug 17, 1999Deposition site: NDB / Processing site: RCSB
Revision 1.0Oct 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
B: 5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
C: 5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
D: 5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7458
Polymers16,3954
Non-polymers3504
Water19811
1
A: 5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1862
Polymers4,0991
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1862
Polymers4,0991
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1862
Polymers4,0991
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1862
Polymers4,0991
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.76, 67.89, 61.83
Angle α, β, γ (deg.)90.0, 96.8, 90.0
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: DNA chain
5'-D(GP*(BRU)P*TP*TP*TP*GP*(S02)*CP*AP*AP*AP*AP*C)-3'


Mass: 4098.678 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: OLIGONUCLEOTIDE, SRCL2, NA-CACODYLATE BUFFER, 2-METHYL-2,4-PENTANEDIOL, pH 6.3, VAPOR DIFFUSION, HANGING DROP at 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1SRCL211
2SODIUM CACODYLATE BUFFER11
3MPD11
4MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.8 mMprotein1drop
240 mMsodium cacodylate1drop
350 mM1dropSrCl2
440 %1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: APS-1 / Detector: CCD / Date: Feb 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.15→30 Å / Num. all: 3434 / Num. obs: 3434 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.097
Reflection shellResolution: 3.15→3.26 Å / Rmerge(I) obs: 0.095 / % possible all: 99
Reflection
*PLUS

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0.5 / Stereochemistry target values: PARKINSON et al.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 202 7 %RANDOM
Rwork0.257 ---
obs0.257 2864 80.1 %-
all-3046 --
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1072 4 11 1087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.71
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 8 Å / σ(F): 0.5 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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