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- PDB-6uf1: Pistol ribozyme transition-state analog vanadate -

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Basic information

Entry
Database: PDB / ID: 6uf1
TitlePistol ribozyme transition-state analog vanadate
Components
  • RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(GVA)*UP*CP*CP*AP*A)-3')
  • RNA (50-MER)
KeywordsRNA / Self-cleaving ribozymes / transesterification reaction / pre-catalytic state / pentavalent transition state analog / cyclophosphate product
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTeplova, M. / Falschlunger, C. / Krasheninina, O. / Patel, D.J. / Micura, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR) United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Crucial Roles of Two Hydrated Mg2+Ions in Reaction Catalysis of the Pistol Ribozyme.
Authors: Teplova, M. / Falschlunger, C. / Krasheninina, O. / Egger, M. / Ren, A. / Patel, D.J. / Micura, R.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (50-MER)
B: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(GVA)*UP*CP*CP*AP*A)-3')
C: RNA (50-MER)
D: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(GVA)*UP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,87921
Polymers41,9454
Non-polymers93417
Water0
1
A: RNA (50-MER)
B: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(GVA)*UP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,46711
Polymers20,9722
Non-polymers4949
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-56 kcal/mol
Surface area10580 Å2
MethodPISA
2
C: RNA (50-MER)
D: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(GVA)*UP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,41210
Polymers20,9722
Non-polymers4408
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-50 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.570, 90.570, 122.558
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: RNA chain RNA (50-MER)


Mass: 16225.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: RNA chain RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(GVA)*UP*CP*CP*AP*A)-3')


Mass: 4746.709 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.05 M HEPES sodium, pH 7.5, 0.1 M manganese chloride, 25% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.8917 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 21, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8917 Å / Relative weight: 1
ReflectionResolution: 2.9→122.6 Å / Num. obs: 10544 / % possible obs: 98.9 % / Redundancy: 8.5 % / Rpim(I) all: 0.046 / Net I/σ(I): 11.2
Reflection shellResolution: 2.9→3.08 Å / Rpim(I) all: 5.326

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.981 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.89
RfactorNum. reflection% reflection
Rfree0.2547 1754 10.07 %
Rwork0.1992 --
obs0.2048 9605 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.19 Å2 / Biso mean: 118.0235 Å2 / Biso min: 82.27 Å2
Refinement stepCycle: final / Resolution: 3.1→19.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2764 17 0 2781
Biso mean--137.22 --
Num. residues----130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.18360.3631350.3326117297
3.1836-3.27680.36971290.3244119596
3.2768-3.38210.36271230.2747120998
3.3821-3.50240.26421320.2517118698
3.5024-3.64180.32651400.249120798
3.6418-3.80650.31310.2164118399
3.8065-4.00560.24251360.1886120999
4.0056-4.25430.22141380.18581214100
4.2543-4.57920.2651350.18881213100
4.5792-5.03330.26111450.19381222100
5.0333-5.74640.2261340.16881211100
5.7464-7.18350.28261360.21031215100
7.1835-19.9810.20961400.17211221100

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