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- PDB-3knc: Crystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(C... -

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Basic information

Entry
Database: PDB / ID: 3knc
TitleCrystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(CGCUACGC)
Components
  • 5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR)P*(XGR)P*(XGR))-3'
  • 5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'
KeywordsRNA/CYCLOHEXENE-RNA HYBRID / cyclohexene / sugar modification / RNA / RNA-CYCLOHEXENE-RNA HYBRID complex
Function / homologyDNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsOvaere, M. / Van Meervelt, L.
CitationJournal: Chemistry / Year: 2011
Title: The Crystal Structure of the CeNA:RNA Hybrid ce(GCGTAGCG):r(CGCUACGC).
Authors: Ovaere, M. / Herdewijn, P. / Van Meervelt, L.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2012Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR)P*(XGR)P*(XGR))-3'
B: 5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4374
Polymers5,3892
Non-polymers492
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-34.1 kcal/mol
Surface area11444 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.919, 41.919, 68.444
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-200-

MG

DetailsBiological unit is the same as asymmetric unit

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Components

#1: DNA chain 5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR)P*(XGR)P*(XGR))-3'


Mass: 2887.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The CeNA strand was synthesized.
#2: RNA chain 5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'


Mass: 2501.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The RNA strand was synthesized.
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1Magnesium formate11
2Magnesium formate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→36.3 Å / Num. all: 2460 / Num. obs: 2575 / % possible obs: 98.8 % / Redundancy: 9.4 % / Rsym value: 0.048

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.9 Å
Translation2.5 Å24.9 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→36.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.762 / SU B: 9.838 / SU ML: 0.19 / SU R Cruickshank DPI: 0.31 / SU Rfree: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.232 114 4.4 %RANDOM
Rwork0.184 ---
obs0.187 2574 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.75 Å2 / Biso mean: 61.046 Å2 / Biso min: 37.01 Å2
Baniso -1Baniso -2Baniso -3
1-4.49 Å22.24 Å20 Å2
2--4.49 Å20 Å2
3----6.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 341 2 47 390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021396
X-RAY DIFFRACTIONr_angle_refined_deg2.2472.972617
X-RAY DIFFRACTIONr_chiral_restr0.120.263
X-RAY DIFFRACTIONr_gen_planes_refined0.010.017199
X-RAY DIFFRACTIONr_mcbond_it0.1081.51
X-RAY DIFFRACTIONr_scbond_it2.8123392
X-RAY DIFFRACTIONr_scangle_it4.3174.5605
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.733 9 -
Rwork0.379 169 -
all-178 -
obs--97.27 %

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