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- PDB-3hr3: Interplay of Structure, Hydration and Thermal Stability in Formac... -

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Basic information

Entry
Database: PDB / ID: 3hr3
TitleInterplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Hydrophobic Modifications Better than DNA
Components5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'
KeywordsDNA / RNA / formacetal-DNA / RNA hydration
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsEgli, M. / Pallan, P.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Interplay of structure, hydration and thermal stability in formacetal modified oligonucleotides: RNA may tolerate nonionic modifications better than DNA.
Authors: Kolarovic, A. / Schweizer, E. / Greene, E. / Gironda, M. / Pallan, P.S. / Egli, M. / Rozners, E.
History
DepositionJun 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 25, 2015Group: Other
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,0111
Polymers3,0111
Non-polymers00
Water41423
1
A: 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'

A: 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0222
Polymers6,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2100 Å2
ΔGint4 kcal/mol
Surface area3470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.199, 33.199, 68.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3'


Mass: 3011.051 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesize deoxyribonucleotide, US4 = Formacetal linked thymidine and 2'-deoxyadenosine (TfA)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium cacodylate (20 mM, pH 6.0), potassium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD 5% v/v) , VAPOR DIFFUSION, ...Details: Sodium cacodylate (20 mM, pH 6.0), potassium chloride (40 mM), magnesium chloride (10 mM), spermine tetrahydrochloride (6 mM), and 2-methyl-2,4-pentanediol (MPD 5% v/v) , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2009 / Details: Monochromator Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 4208 / Num. obs: 4006 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Redundancy: 17 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.187 / Num. unique all: 139 / % possible all: 72.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Single strand from the duplex of PDB ID 411D.

411d


Resolution: 1.75→29.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.139 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28185 291 7.3 %RANDOM
Rwork0.22786 ---
obs0.23147 3714 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.242 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 201 0 23 224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021225
X-RAY DIFFRACTIONr_angle_refined_deg3.0372.974344
X-RAY DIFFRACTIONr_chiral_restr0.120.239
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02104
X-RAY DIFFRACTIONr_scbond_it3.5153225
X-RAY DIFFRACTIONr_scangle_it4.5194.5343
X-RAY DIFFRACTIONr_rigid_bond_restr3.283225
X-RAY DIFFRACTIONr_sphericity_free7.99329
X-RAY DIFFRACTIONr_sphericity_bonded6.0833201
LS refinement shellResolution: 1.753→1.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 19 -
Rwork0.376 199 -
obs--73.65 %

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