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- PDB-3ftm: Class II ligase ribozyme product-template duplex, structure 1 -

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Basic information

Entry
Database: PDB / ID: 3ftm
TitleClass II ligase ribozyme product-template duplex, structure 1
Components
  • 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3'
  • 5'-R(*GP*UP*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 / Resolution: 2.7 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 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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*UP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'
B: 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3'
C: 5'-R(*GP*UP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'
D: 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,12415
Polymers14,8274
Non-polymers29711
Water1086
1
A: 5'-R(*GP*UP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'
B: 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5598
Polymers7,4142
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-46 kcal/mol
Surface area4260 Å2
MethodPISA
2
C: 5'-R(*GP*UP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'
D: 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5657
Polymers7,4142
Non-polymers1515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-31 kcal/mol
Surface area4290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.550, 31.550, 171.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 3579.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template stand of the class II ligase a4-11
#2: RNA chain 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3'


Mass: 3834.376 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Product strand of the 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.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 mM RNA duplex, 10mM magnesium chloride, 200mM magnesium acetate, 15% PEG 8000, 50mM cacodylate pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium chloride11
2magnesium acetate11
3PEG 800011
4cacodylateCacodylic acid11
5magnesium chloride12
6magnesium acetate12
7PEG 800012
8cacodylateCacodylic acid12

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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: May 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 4565 / % possible obs: 98.7 % / Observed criterion σ(I): 4 / Redundancy: 3.8 % / Biso Wilson estimate: 92.9 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 29.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.9 / Num. unique all: 458 / Rsym value: 0.442 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.7→29.6 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 141151.41 / 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
Rfree0.268 467 10.6 %RANDOM
Rwork0.218 ---
obs0.218 4423 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å20 Å2
2--2.81 Å20 Å2
3----5.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 982 11 6 999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d14.1
X-RAY DIFFRACTIONc_improper_angle_d1.6
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.444 75 10.7 %
Rwork0.436 623 -
obs--91 %
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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