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- PDB-6ufk: Pistol ribozyme product crystal soaked in Mn2+ -

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Basic information

Entry
Database: PDB / ID: 6ufk
TitlePistol ribozyme product crystal soaked in Mn2+
Components
  • RNA (5'-R(*UP*CP*CP*AP*G)-3')
  • RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-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 speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Feb 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 1.4Mar 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*(23G))-3')
E: RNA (5'-R(*UP*CP*CP*AP*G)-3')
C: RNA (50-MER)
D: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3')
F: RNA (5'-R(*UP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,68228
Polymers42,4736
Non-polymers1,20922
Water0
1
A: RNA (50-MER)
B: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3')
E: RNA (5'-R(*UP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,78613
Polymers21,2373
Non-polymers54910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-55 kcal/mol
Surface area10550 Å2
MethodPISA
2
C: RNA (50-MER)
D: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3')
F: RNA (5'-R(*UP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,89615
Polymers21,2373
Non-polymers65912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-68 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.346, 90.346, 121.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11E-101-

MN

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Components

#1: RNA chain RNA (50-MER)


Mass: 16537.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3')


Mass: 3152.809 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*UP*CP*CP*AP*G)-3')


Mass: 1545.984 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 22 / 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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: grown in 0.05 M HEPES sodium, pH 7.5, 0.1 M magnesium chloride, 25-30% MPD, soaked in 0.05 M HEPES sodium, pH 7.5, 0.1 M manganese(II) chloride, 35% 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: 2.97→90.4 Å / Num. obs: 9562 / % possible obs: 99.2 % / Redundancy: 5.9 % / Rpim(I) all: 0.052 / Net I/σ(I): 11.3
Reflection shellResolution: 2.97→3.15 Å / Num. unique obs: 9982 / Rpim(I) all: 33.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.929 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.72
RfactorNum. reflection% reflection
Rfree0.2571 1539 9.98 %
Rwork0.2109 --
obs0.2156 8567 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.85 Å2 / Biso mean: 134.3903 Å2 / Biso min: 93.45 Å2
Refinement stepCycle: final / Resolution: 3.2→19.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2764 22 0 2786
Biso mean--144.51 --
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 (%)
3.2001-3.3030.46991370.4407124396
3.303-3.42050.42471420.3766122796
3.4205-3.55670.39561330.3219123695
3.5567-3.71760.38681370.293122595
3.7176-3.91220.31341390.2332125896
3.9122-4.15520.24071440.2104126799
4.1552-4.47270.22221440.2037129099
4.4727-4.91670.27361360.1983128798
4.9167-5.61420.25871440.17561301100
5.6142-7.02150.27681330.2006127899
7.0215-19.9290.18981500.1764127499

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