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- PDB-3b58: Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation ... -

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Basic information

Entry
Database: PDB / ID: 3b58
TitleMinimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and a 2',5'-Phosphodiester Linkage at the Active Site
Components
  • 29-mer Loop A and Loop B Ribozyme strand
  • Loop A Substrate strand
  • Loop B S-turn strand
KeywordsRNA / hairpin ribozyme / 2' / 5' phosphodiester
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsMacElrevey, C. / Krucinska, J. / Wedekind, J.E.
CitationJournal: Rna / Year: 2008
Title: Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
Authors: MacElrevey, C. / Salter, J.D. / Krucinska, J. / Wedekind, J.E.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...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 / struct_conn / struct_ref_seq
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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Loop A Substrate strand
B: 29-mer Loop A and Loop B Ribozyme strand
C: Loop B S-turn strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2416
Polymers19,8233
Non-polymers4183
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-28 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.370, 93.370, 132.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain Loop A Substrate strand


Mass: 4052.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid-phase synthesis at Keck Institute, Yale
#2: RNA chain 29-mer Loop A and Loop B Ribozyme strand


Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid phase chemical synthesis at Dharmacon, Colorado
#3: RNA chain Loop B S-turn strand


Mass: 6007.568 Da / Num. of mol.: 1 / Mutation: A38G, U39C / Source method: obtained synthetically
Details: solid phase chemical synthesis at Dharmacon, Colorado

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Non-polymers , 3 types, 14 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.2 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 2K MME, lithium sulfate, HEPES, spermidine, cobalt hexaammine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2K MME11
2Li2SO411
3HEPES11
4spermidine11
5cobalt hexaammine11
6PEG 2K MME12
7Li2SO412
8HEPES12
9spermidine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2007 / Details: cylindrically bent rhodium-coated silicon mirror
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.65→29.8 Å / Num. all: 10426 / Num. obs: 10328 / % possible obs: 99.1 % / Redundancy: 10.2 % / Biso Wilson estimate: 57.2 Å2 / Rsym value: 0.057 / Net I/σ(I): 20.7
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1020 / Rsym value: 0.047 / % possible all: 99.4

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Processing

Software
NameClassification
Adxvdata processing
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2P7F

2p7f


Resolution: 2.65→29.8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 407319.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 958 9.3 %RANDOM
Rwork0.236 ---
all0.237 10426 --
obs0.237 10312 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.8997 Å2 / ksol: 0.308089 e/Å3
Displacement parametersBiso mean: 84.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.19 Å2-12.86 Å20 Å2
2---10.19 Å20 Å2
3---20.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-29.8 Å
Luzzati sigma a0.51 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.65→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1390 19 11 1420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d1.98
LS refinement shellResolution: 2.65→2.92 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.615 235 9.3 %
Rwork0.608 2294 -
obs-2529 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramdna-rna0107.top
X-RAY DIFFRACTION2dna-rna0107.parwater.top
X-RAY DIFFRACTION3cobalt.parcobalt.top
X-RAY DIFFRACTION4ion.paramion.top

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