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- PDB-2p7d: A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics... -

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Basic information

Entry
Database: PDB / ID: 2p7d
TitleA Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution
Components
  • (Ribozyme strand ...) x 3
  • 3' substrate strand, octameric fragment
  • 5' substrate strand, pentameric fragment
KeywordsRNA / hairpin ribozyme / product mimic / transition-state stabilization / active site waters / induced fit
Function / homologyCOBALT HEXAMMINE(III) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsTorelli, A.T. / Krucinska, J. / Wedekind, J.E.
Citation
Journal: Rna / Year: 2007
Title: A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization
Authors: Torelli, A.T. / Krucinska, J. / Wedekind, J.E.
#1: 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. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E.
#2: 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
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_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' substrate strand, pentameric fragment
B: Ribozyme strand I
C: Ribozyme strand II
D: Ribozyme strand III
P: 3' substrate strand, octameric fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1589
Polymers19,7175
Non-polymers4414
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.9, 93.9, 134.4
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number178
Space group name H-MP6122
DetailsThe ribozyme-substrate complex in the asymmetric unit also represents the biological unit

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Components

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RNA chain , 2 types, 2 molecules AP

#1: RNA chain 5' substrate strand, pentameric fragment


Mass: 1505.960 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in tobacco ringspot virus satellite RNA
#5: RNA chain 3' substrate strand, octameric fragment


Mass: 2501.553 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in tobacco ringspot virus satellite RNA

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Ribozyme strand ... , 3 types, 3 molecules BCD

#2: DNA/RNA hybrid Ribozyme strand I


Mass: 4182.585 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in tobacco ringspot virus satellite RNA
#3: RNA chain Ribozyme strand II


Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in tobacco ringspot virus satellite RNA
#4: RNA chain Ribozyme strand III


Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in tobacco ringspot virus satellite RNA

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Non-polymers , 4 types, 41 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


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


Mass: 18.015 Da / Num. of mol.: 37 / 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: 4.32 Å3/Da / Density % sol: 80.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 250 mM Li2SO4, 2.5 mM [Co(NH3)6]Cl3, 2 mM spermidine-HCl, 20 mM NAF, 50 mM ascorbic acid, 100 mM sodium cacodylate buffer and 18.5% PEG 2000 MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Li2SO411
2[Co(NH3)6]Cl311
3spermidine-HCl11
4NAF11
5ascorbic acid11
6sodium cacodylate11
7PEG 2000 MME11
8Li2SO412
9spermidine-HCl12
10PEG 2000 MME12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2006
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.25→40.64 Å / Num. all: 16622 / Num. obs: 16622 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 7.24 % / Biso Wilson estimate: 86.9 Å2 / Rsym value: 0.045 / Net I/σ(I): 23.2
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.95 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.434 / % possible all: 95.5

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1ZFR

1zfr
PDB Unreleased entry


Resolution: 2.25→30.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 948513.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: Parkinson et al. Acta Cryst.D,52,57 (1996)
RfactorNum. reflection% reflectionSelection details
Rfree0.237 811 4.9 %RANDOM
Rwork0.229 ---
all0.2291 16605 --
obs0.2291 16605 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.2658 Å2 / ksol: 0.337924 e/Å3
Displacement parametersBiso mean: 78.7 Å2
Baniso -1Baniso -2Baniso -3
1--11.93 Å2-3.49 Å20 Å2
2---11.93 Å20 Å2
3---23.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.47 Å
Luzzati d res low-40.64 Å
Luzzati sigma a0.62 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.25→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1347 20 37 1404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.442 148 5.5 %
Rwork0.454 2535 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rnaATTdna-rnaATT
X-RAY DIFFRACTION2cobalt.parcobalt.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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