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- PDB-3cr1: crystal structure of a minimal, mutant, all-RNA hairpin ribozyme ... -

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Basic information

Entry
Database: PDB / ID: 3cr1
Titlecrystal structure of a minimal, mutant, all-RNA hairpin ribozyme (A38C, A-1OMA) grown from MgCl2
Components
  • RNA (5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3')
  • RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*CP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')
  • loop A and B ribozyme strand
KeywordsRNA / ribozyme / A38
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsSalter, J.D. / 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
DepositionApr 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq / 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_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_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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: RNA (5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3')
B: loop A and B ribozyme strand
C: RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*CP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9175
Polymers19,7973
Non-polymers1202
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-25 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.640, 93.640, 133.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1-

U

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Components

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RNA chain , 2 types, 2 molecules AC

#1: RNA chain RNA (5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3')


Mass: 4066.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 13-mer substrate strand
#3: RNA chain RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*CP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')


Mass: 5967.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: loop B ribozyme strand

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DNA/RNA hybrid , 1 types, 1 molecules B

#2: DNA/RNA hybrid loop A and B ribozyme strand


Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 35 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.27 Å3/Da / Density % sol: 71.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG2000 MME, lithium sulfate, magnesium chloride, spermidine, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG2000 MME11
2lithium sulfate11
3magnesium chloride11
4spermidine11
5sodium cacodylate11
6PEG2000 MME12
7lithium sulfate12
8magnesium chloride12
9spermidine12
10sodium cacodylate12

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 20, 2007
RadiationMonochromator: bent triangular asymmetric cut si(111) monochromator, RH-coated si for vertical focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.25→30.89 Å / Num. obs: 16729 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 11.01 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 4.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2OUE

2oue


Resolution: 2.25→30.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 941903.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
Stereochemistry target values: Parkinson et al. Acta Cryst. D, 52, 57-64 (1996)
Details: Bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1314 7.9 %RANDOM
Rwork0.219 ---
all0.221 ---
obs-16725 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9068 Å2 / ksol: 0.335642 e/Å3
Displacement parametersBiso mean: 68.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.35 Å2-4.64 Å20 Å2
2---7.35 Å20 Å2
3---14.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.25→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1309 6 33 1348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_improper_angle_d2.22
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 215 7.8 %
Rwork0.414 2538 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna0107.pardna-rna0107.top
X-RAY DIFFRACTION2water.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.param

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