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- PDB-6ufj: Pistol ribozyme product crystal structure -

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Basic information

Entry
Database: PDB / ID: 6ufj
TitlePistol ribozyme product crystal structure
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 / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.645 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)42,88723
Polymers42,4736
Non-polymers41317
Water362
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)21,45512
Polymers21,2373
Non-polymers2199
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-72 kcal/mol
Surface area10390 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)21,43111
Polymers21,2373
Non-polymers1948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-66 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.734, 90.734, 121.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 50
211chain CC1 - 50
112chain BB1 - 15
212chain DD1 - 15

NCS ensembles :
ID
1
2

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.05 M HEPES sodium, pH 7.5, 0.1 M magnesium chloride, 25-30% 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: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.645→50 Å / Num. obs: 15346 / % possible obs: 99.8 % / Redundancy: 11.2 % / Rpim(I) all: 0.015 / Net I/σ(I): 43.1
Reflection shellResolution: 2.65→2.7 Å / Num. unique obs: 723 / Rpim(I) all: 0.28

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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: 2.645→38.493 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.86
RfactorNum. reflection% reflection
Rfree0.2391 1519 10 %
Rwork0.1901 --
obs0.195 15194 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.54 Å2 / Biso mean: 91.9876 Å2 / Biso min: 49.05 Å2
Refinement stepCycle: final / Resolution: 2.645→38.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2764 17 2 2783
Biso mean--87.44 72.13 -
Num. residues----130
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1192X-RAY DIFFRACTION7.799TORSIONAL
12C1192X-RAY DIFFRACTION7.799TORSIONAL
21B332X-RAY DIFFRACTION7.799TORSIONAL
22D332X-RAY DIFFRACTION7.799TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6453-2.73060.43421240.3786113191
2.7306-2.82820.53131360.3261122499
2.8282-2.94140.32891330.2939121899
2.9414-3.07520.35621370.2733121398
3.0752-3.23730.25191360.2245122397
3.2373-3.440.24851340.1973120698
3.44-3.70540.24351410.18821258100
3.7054-4.07790.18541390.1568125099
4.0779-4.66710.20331410.15211280100
4.6671-5.87670.22321450.16711295100
5.8767-38.4930.22971530.1883137799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.242-0.43020.81920.76230.58494.0417-0.2051-0.06470.19830.005-0.13570.3168-1.21760.42380.33861.25830.0669-0.12750.6163-0.0160.6739203.3762222.7444135.8415
20.3711-0.00210.59140.1712-0.04250.9308-0.19790.50830.2948-0.74290.00330.0019-1.75291.15080.10311.5942-0.2856-0.20551.30130.01370.803213.8373229.5806142.5385
30.68190.2005-0.37772.93630.06892.9318-0.2428-0.06210.34790.00220.2318-0.0211-0.2407-0.82270.01720.64230.2915-0.13960.8487-0.05820.6717179.6318202.0176109.8208
40.96890.0785-1.02132.660.10881.9268-0.24340.11680.1569-0.16160.25070.1350.4088-1.1698-0.07390.68830.0361-0.060.9445-0.04390.5142172.6451192.9696101.4341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 50 )A1 - 50
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 15 )B1 - 15
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 50 )C1 - 50
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 15 )D1 - 15

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