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

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Basic information

Entry
Database: PDB / ID: 6uey
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 / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)42,16413
Polymers41,9454
Non-polymers2199
Water00
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)21,0706
Polymers20,9722
Non-polymers974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-37 kcal/mol
Surface area10520 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)21,0947
Polymers20,9722
Non-polymers1225
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-46 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.829, 91.829, 123.444
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:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AAGGchain AAA1 - 501 - 50
21AAGGchain CCC1 - 501 - 50
12UUAAchain BBB1 - 151 - 15
22UUAAchain DDD1 - 151 - 15

NCS ensembles :
ID
1
2

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg

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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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium acetate, pH 4.6, 0.02 M calcium 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-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2019
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→45.9 Å / Num. obs: 13611 / % possible obs: 99.8 % / Redundancy: 10.2 % / CC1/2: 0.987 / Net I/σ(I): 37.9
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 675 / Rpim(I) all: 0.017

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.652 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.84
RfactorNum. reflection% reflection
Rfree0.2515 1325 9.96 %
Rwork0.2118 --
obs0.2157 13303 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 218.17 Å2 / Biso mean: 120.3043 Å2 / Biso min: 70.27 Å2
Refinement stepCycle: final / Resolution: 2.8→19.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2764 9 0 2773
Biso mean--87.3 --
Num. residues----130
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1192X-RAY DIFFRACTION5.929TORSIONAL
12C1192X-RAY DIFFRACTION5.929TORSIONAL
21B340X-RAY DIFFRACTION5.929TORSIONAL
22D340X-RAY DIFFRACTION5.929TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8002-2.9120.41211440.3499128498
2.912-3.04410.39641360.3224129598
3.0441-3.20390.32361430.3015129597
3.2039-3.40370.27311440.2462127096
3.4037-3.66490.26581470.2263132198
3.6649-4.03090.1941440.198131799
4.0309-4.60760.24471520.19741364100
4.6076-5.78040.22241520.19261373100
5.7804-19.6520.2491630.19021459100
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)
15.5433-0.1053.6621.82650.49357.7577-0.02850.05490.2493-0.0411-0.28070.0796-0.77771.36680.32891.90630.2228-0.0771.0028-0.00110.5898205.2212133.3237137.7233
23.32121.58080.71942.3753-0.34761.3250.41430.5461.1621-1.4349-0.0949-0.2243-1.90332.1186-0.17812.2122-0.1944-0.09161.97760.02810.8065215.3749140.098144.8307
32.42380.734-0.554.8904-0.24643.6110.08640.56480.37560.62810.1873-0.18320.7227-0.4043-0.25861.46060.5085-0.19790.9686-0.00270.623181.4217112.8014111.5677
42.38251.5129-2.52931.0409-1.58572.71270.15651.0695-0.04370.49410.63450.80461.7634-0.8045-0.65032.25620.3019-0.18691.28540.05260.5617174.7021104.3235102.8206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 51)A1 - 50
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 15)B1 - 15
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 51)C1 - 50
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 15)D1 - 15

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