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- PDB-2p7f: The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Int... -

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Basic information

Entry
Database: PDB / ID: 2p7f
TitleThe Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme
Components
  • Loop A ribozyme strand
  • Loop B S-turn strand
  • Loop B ribozyme strand
  • substrate strand
KeywordsRNA / hairpin ribozyme / 2' / 5' phosphodiester / vanadate / reaction intermediate / transition-state stabilization / active site waters / induced fit
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_comp_id / _struct_conn.ptnr2_label_seq_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: substrate strand
B: Loop A ribozyme strand
C: Loop B ribozyme strand
D: Loop B S-turn strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9527
Polymers19,5344
Non-polymers4183
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.1, 94.1, 127.2
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 , 4 types, 4 molecules ABCD

#1: RNA chain substrate strand


Mass: 4036.471 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in tobacco ringspot virus satellite RNA
#2: RNA chain Loop A ribozyme strand


Mass: 3970.448 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in tobacco ringspot virus satellite RNA
#3: RNA chain Loop B ribozyme strand


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 Loop B S-turn strand


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 , 3 types, 18 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 4.11 Å3/Da / Density % sol: 79.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 250 mM Li2SO4, 2.5 mM [Co(NH3)6]Cl3, 2 mM spermidine-HCl, 15 mM nicotinic acid, 100 mM sodium HEPES buffer and 20.5% PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Li2SO411
2[Co(NH3)6]Cl311
3spermidine-HCl11
4nicotinic acid11
5sodium HEPES11
6PEG 2000 MME11
7Li2SO412
8spermidine-HCl12
9PEG 2000 MME12
10sodium HEPES12

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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: 2.35→40.76 Å / Num. all: 14321 / Num. obs: 14321 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.92 % / Biso Wilson estimate: 90.5 Å2 / Rsym value: 0.037 / Net I/σ(I): 19.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.32 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.448 / % possible all: 99.1

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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: 2.35→29.38 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 776924.6 / 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
Rfree0.252 724 5.1 %RANDOM
Rwork0.227 ---
all0.226 14313 --
obs0.226 14313 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 81.7 Å2
Baniso -1Baniso -2Baniso -3
1--13.01 Å2-2.59 Å20 Å2
2---13.01 Å20 Å2
3---26.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.48 Å
Luzzati d res low-40.76 Å
Luzzati sigma a0.67 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1310 19 15 1344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_improper_angle_d1.86
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.516 113 4.9 %
Rwork0.475 2203 -
obs--99.1 %
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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