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- PDB-5dek: RNA octamer containing dT -

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Basic information

Entry
Database: PDB / ID: 5dek
TitleRNA octamer containing dT
ComponentsRNA oligonucleotide containing dT
KeywordsRNA / oligonucleotide
Function / homologyCOBALT HEXAMMINE(III) / DNA/RNA hybrid
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.993 Å
AuthorsHarp, J.M. / Egli, M.
CitationJournal: J.Org.Chem. / Year: 2016
Title: Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides.
Authors: Kel In, A.V. / Zlatev, I. / Harp, J. / Jayaraman, M. / Bisbe, A. / O Shea, J. / Taneja, N. / Manoharan, R.M. / Khan, S. / Charisse, K. / Maier, M.A. / Egli, M. / Rajeev, K.G. / Manoharan, M.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA oligonucleotide containing dT
B: RNA oligonucleotide containing dT
C: RNA oligonucleotide containing dT
D: RNA oligonucleotide containing dT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4216
Polymers10,0984
Non-polymers3222
Water1,18966
1
A: RNA oligonucleotide containing dT
B: RNA oligonucleotide containing dT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2103
Polymers5,0492
Non-polymers1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-5 kcal/mol
Surface area3210 Å2
MethodPISA
2
C: RNA oligonucleotide containing dT
D: RNA oligonucleotide containing dT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2103
Polymers5,0492
Non-polymers1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-4 kcal/mol
Surface area3210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.059, 44.059, 85.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: DNA/RNA hybrid
RNA oligonucleotide containing dT


Mass: 2524.588 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 20 mM MgCl2, 80 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionRedundancy: 12.8 % / Number: 77578 / Rmerge(I) obs: 0.126 / Χ2: 1.06 / D res high: 2 Å / D res low: 50 Å / Num. obs: 6070 / % possible obs: 97.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.435010.0811.11611.3
4.315.4310.0811.06812.9
3.764.3110.0951.06913.3
3.423.7610.1171.0713.7
3.173.4210.1321.05513.7
2.993.1710.1641.17513.6
2.842.9910.1891.17514.1
2.712.8410.2541.17313.9
2.612.7110.2541.17514.3
2.522.6110.3561.07114
2.442.5210.461.02114.1
2.372.4410.5720.98114.2
2.312.3710.630.99214.2
2.252.3110.7450.97814.2
2.22.2510.9120.99313.7
2.152.210.9970.99712.7
2.112.1510.94811.6
2.072.1110.9919.7
2.032.0710.940.988.7
22.0310.9741.0627.5
ReflectionResolution: 2→39.15 Å / Num. obs: 10680 / % possible obs: 97.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 40.4550168222 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.038 / Rrim(I) all: 0.128 / Χ2: 1.059 / Net I/av σ(I): 15.113 / Net I/σ(I): 7.5 / Num. measured all: 77578
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.037.50.6821.8196.6
2.03-2.078.70.94197.3
2.07-2.119.7197
2.11-2.1511.6197
2.15-2.212.70.997197
2.2-2.2513.70.912197.1
2.25-2.3114.20.745197.3
2.31-2.3714.20.63197.3
2.37-2.4414.20.572197.7
2.44-2.5214.10.46198
2.52-2.61140.356198.1
2.61-2.7114.30.254198.3
2.71-2.8413.90.254197.7
2.84-2.9914.10.189197.8
2.99-3.1713.60.164197.2
3.17-3.4213.70.132197.1
3.42-3.7613.70.117197.8
3.76-4.3113.30.095198.4
4.31-5.4312.90.081198.8
5.43-5011.30.081197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v706edata collection
HKL-2000v706edata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000v706edata reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.993→39.155 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.41 / Phase error: 34.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 559 5.23 %
Rwork0.24 10121 -
obs0.2411 10680 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.87 Å2 / Biso mean: 41.8983 Å2 / Biso min: 30.29 Å2
Refinement stepCycle: final / Resolution: 1.993→39.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 668 14 66 748
Biso mean--66.91 49.56 -
Num. residues----32
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001756
X-RAY DIFFRACTIONf_angle_d0.3031182
X-RAY DIFFRACTIONf_chiral_restr0.01152
X-RAY DIFFRACTIONf_plane_restr0.00132
X-RAY DIFFRACTIONf_dihedral_angle_d4.952360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9931-2.19370.3981450.32422500264597
2.1937-2.51110.34371420.30382546268898
2.5111-3.16350.25621340.29242557269198
3.1635-39.16250.22751380.18942518265697

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