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- PDB-3fs0: Class II ligase ribozyme product-template duplex, structure 2 -

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Basic information

Entry
Database: PDB / ID: 3fs0
TitleClass II ligase ribozyme product-template duplex, structure 2
Components
  • 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*C)-3'
  • 5'-R(*GP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'
KeywordsRNA / ribozyme / ligase / 2'-5' / 2-5 / 2p5
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPitt, J.N. / Ferre-D'Amare, A.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structure-guided engineering of the regioselectivity of RNA ligase ribozymes.
Authors: Pitt, J.N. / Ferre-D'Amare, A.R.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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'-R(*GP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'
B: 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9007
Polymers6,7782
Non-polymers1225
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-38 kcal/mol
Surface area4030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.040, 30.040, 59.666
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: RNA chain 5'-R(*GP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'


Mass: 3272.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template strand of Class II ligase A4-11 / References: GenBank: U26406
#2: RNA chain 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*C)-3'


Mass: 3505.170 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Product strand of Class II ligase A4-11, single stranded RNA with one 2'-5' linkage
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2mM RNA duplex, 10mM MgCl2, 25% PEG 4000, 0.2M lithium sulfate, 100mM Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2PEG 400011
3lithium sulfate11
4Tris11
5MgCl212
6PEG 400012
7lithium sulfate12
8Tris12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 2663 / % possible obs: 99.5 % / Observed criterion σ(I): 4 / Redundancy: 5.7 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 31.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.6 / Num. unique all: 242 / Rsym value: 0.307 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FTM

3ftm


Resolution: 2.3→23.85 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 436790.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 252 9.5 %RANDOM
Rwork0.208 ---
obs0.208 2653 99.7 %-
all-2661 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.78 Å210.5 Å20 Å2
2--9.78 Å20 Å2
3----19.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.3→23.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 449 5 12 466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d14.9
X-RAY DIFFRACTIONc_improper_angle_d1.76
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 38 9.1 %
Rwork0.36 378 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2pitt.parampitt.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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