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- PDB-1zfv: The structure of an all-RNA minimal Hairpin Ribozyme with Mutatio... -

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Basic information

Entry
Database: PDB / ID: 1zfv
TitleThe structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site
Components
  • 5'-R(*CP*GP*GP*UP*GP*AP*AP*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 / HAIRPIN RIBOZYME / ALL-RNA / COBALT HEXAAMINE / MUTATION / JUNCTIONLESS / LOW SALT / S-TURN / E-LOOP / RIBOSE ZIPPER / CATALYTIC RNA
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsWedekind, 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. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and x-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme
Authors: Grum-Tokars, V. / Milovanovic, M. / Wedekind, J.E.
#2: Journal: Embo J. / Year: 2001
Title: Functional involvement of G8 in the hairpin ribozyme cleavage mechanism
Authors: Pinard, R. / Hampel, K.J. / Heckman, J.E. / Lambert, D. / Chan, P.A. / Major, F. / Burke, J.M.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*AP*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)19,7916
Polymers19,5344
Non-polymers2572
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.510, 93.510, 124.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe asymmetric unit comprises strands A, B, C and D, which form the biological unit

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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 / Details: Derived from Satellite Tobacco Ringspot Virus
#2: RNA chain 5'-R(*CP*GP*GP*UP*GP*AP*AP*AP*AP*GP*GP*G)-3'


Mass: 3954.448 Da / Num. of mol.: 1 / Mutation: G8A / Source method: obtained synthetically / Details: Derived from Satellite Tobacco Ringspot Virus
#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 / Details: Derived from Satellite Tobacco Ringspot Virus
#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 / Details: Derived from Satellite Tobacco Ringspot Virus

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Non-polymers , 3 types, 36 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2000 MME, LITHIUM SULFATE, SPERMIDINE, COBALT HEXAAMINE , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2000 MME11
2LITHIUM SULFATE11
3SPERMIDINE11
4COBALT HEXAAMINEHexamminecobalt(III) chloride11
5H2O11
6LITHIUM SULFATE12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2004
Details: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING
RadiationMonochromator: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→44 Å / Num. obs: 13112 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 11.9 % / Biso Wilson estimate: 74.3 Å2 / Rsym value: 0.045 / Net I/σ(I): 27.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 11 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.428 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1ZFR

1zfr
PDB Unreleased entry


Resolution: 2.4→43.77 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1305392.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -5 / Stereochemistry target values: CNS / Details: MLI TARGET USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1214 9.3 %RANDOM
Rwork0.243 ---
obs0.243 13109 99.7 %-
all-13112 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.2932 Å2 / ksol: 0.349546 e/Å3
Displacement parametersBiso mean: 74.9 Å2
Baniso -1Baniso -2Baniso -3
1--13.47 Å2-4.46 Å20 Å2
2---13.47 Å20 Å2
3---26.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.44 Å
Luzzati d res low-44 Å
Luzzati sigma a0.82 Å0.82 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1310 12 34 1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d2.19
X-RAY DIFFRACTIONc_mcbond_it1.712.5
X-RAY DIFFRACTIONc_mcangle_it2.963.5
X-RAY DIFFRACTIONc_scbond_it2.343
X-RAY DIFFRACTIONc_scangle_it4.284
LS refinement shellResolution: 2.4→2.64 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.532 306 9.6 %
Rwork0.554 2878 -
obs--100 %
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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