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- PDB-2bcy: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (... -

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Basic information

Entry
Database: PDB / ID: 2bcy
TitleCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)
Components
  • 5'-R(*CP*GP*GP*UP*GP*AP*(MTU)P*AP*AP*GP*GP*G)-3'
  • 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
  • 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'
  • 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
KeywordsRNA / ribozyme / G8 / MTU
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsSalter, J.D. / Wedekind, J.E.
Citation
Journal: Biochemistry / Year: 2006
Title: Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer.
Authors: Salter, J.D. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E.
#1: Journal: Biochemistry / Year: 2005
Title: Conformational Heterogeneity at Position U37 of an all-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn
Authors: Alam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'
B: 5'-R(*CP*GP*GP*UP*GP*AP*(MTU)P*AP*AP*GP*GP*G)-3'
C: 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
D: 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6955
Polymers19,5344
Non-polymers1611
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.900, 93.900, 129.180
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 , 4 types, 4 molecules ABCD

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


Mass: 4052.470 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*CP*GP*GP*UP*GP*AP*(MTU)P*AP*AP*GP*GP*G)-3'


Mass: 3954.448 Da / Num. of mol.: 1 / Mutation: G8(MTU) / Source method: obtained synthetically
#3: RNA chain 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'


Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: RNA chain 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'


Mass: 5991.568 Da / Num. of mol.: 1 / Mutation: U39C / Source method: obtained synthetically

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Non-polymers , 2 types, 12 molecules

#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / 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: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: PEG2000 MME, lithium sulfate, spermidine, cobalt hexamine, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG2000 MME11
2lithium sulfate11
3spermidine11
4cobalt hexamine11
5H2O11
6PEG2000 MME12
7lithium sulfate12
8cobalt hexamine12

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005
RadiationMonochromator: bent triangular asymmetric cut si(111) monochromator, RH-coated si for vertical focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.7→38.78 Å / Num. all: 9556 / Num. obs: 9556 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 97.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8.42 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1ZFR

1zfr
PDB Unreleased entry


Resolution: 2.7→38.06 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 624132.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: CNS 1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.27 604 6.3 %RANDOM
Rwork0.244 ---
all0.245 9550 --
obs0.244 9550 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 117.497 Å2 / ksol: 0.419586 e/Å3
Displacement parametersBiso mean: 81.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.67 Å2-6.63 Å20 Å2
2---14.67 Å20 Å2
3---29.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.52 Å
Luzzati d res low-39 Å
Luzzati sigma a0.89 Å0.83 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1310 7 11 1328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_improper_angle_d2.11
LS refinement shellResolution: 2.7→2.97 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.485 152 6.4 %
Rwork0.527 2208 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ion.paramdna-rna.top
X-RAY DIFFRACTION2dna-rna_rep.paramcobalt.top
X-RAY DIFFRACTION3cobalt.parion.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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