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- PDB-5ktj: Crystal structure of Pistol, a class of self-cleaving ribozyme -

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Basic information

Entry
Database: PDB / ID: 5ktj
TitleCrystal structure of Pistol, a class of self-cleaving ribozyme
Components
  • Pistol (50-MER)
  • RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*GP*UP*CP*CP*AP*A)-3')
KeywordsRNA / ribozyme / self-cleavage / internal transesterification
Function / homologyCOBALT HEXAMMINE(III) / SAMARIUM (III) ION / RNA / RNA (> 10)
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.97 Å
AuthorsNguyen, L.A. / Wang, J. / Steitz, T.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5F32AI114095-02 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structure of Pistol, a class of self-cleaving ribozyme.
Authors: Nguyen, L.A. / Wang, J. / Steitz, T.A.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references / Structure summary
Revision 1.3Feb 15, 2017Group: Database references
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,67943
Polymers42,1034
Non-polymers3,57739
Water1,45981
1
A: Pistol (50-MER)
B: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*GP*UP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,98922
Polymers21,0512
Non-polymers1,93720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-97 kcal/mol
Surface area10900 Å2
MethodPISA
2
C: Pistol (50-MER)
D: RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*GP*UP*CP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,69121
Polymers21,0512
Non-polymers1,63919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-90 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.190, 85.190, 256.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-104-

SM

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Components

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RNA chain , 2 types, 4 molecules ACBD

#1: RNA chain Pistol (50-MER)


Mass: 16385.656 Da / Num. of mol.: 2 / Mutation: dG10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: metagenome (others)
#2: RNA chain RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*GP*UP*CP*CP*AP*A)-3')


Mass: 4665.786 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: metagenome (others)

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Non-polymers , 4 types, 120 molecules

#3: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Sm
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CoH18N6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 6% MPD, 0.02 M magnesium chloride, 0.02 M cobalt hexammine, 0.04 M sodium cacodylate

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.8445, 1.0163,1.8450
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2016
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.84451
21.01631
31.8451
ReflectionResolution: 2.971→81.27 Å / Num. all: 10223 / Num. obs: 10205 / % possible obs: 99.8 % / Redundancy: 17.36 % / Net I/σ(I): 11.87
Reflection shellHighest resolution: 2.971 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.97→81.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 39.314 / SU ML: 0.374 / Cross valid method: THROUGHOUT / ESU R Free: 0.429
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25719 523 5.1 %RANDOM
Rwork0.19559 ---
obs0.19834 9769 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 123.508 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å20 Å2
2--0.73 Å2-0 Å2
3----1.47 Å2
Refinement stepCycle: 1 / Resolution: 2.97→81.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2786 165 15 2966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123238
X-RAY DIFFRACTIONr_bond_other_d0.0050.021463
X-RAY DIFFRACTIONr_angle_refined_deg2.2121.4185163
X-RAY DIFFRACTIONr_angle_other_deg1.72133461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021542
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02684
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0659.6023238
X-RAY DIFFRACTIONr_scbond_other7.0569.5983233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.80914.5665154
X-RAY DIFFRACTIONr_long_range_B_refined15.00393.3854444
X-RAY DIFFRACTIONr_long_range_B_other14.80493.3024442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.971→3.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 40 -
Rwork0.398 703 -
obs--99.2 %
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)
11.89241.079-0.82070.8926-0.2291.143-0.05020.08510.2465-0.0391-0.32560.41020.1757-0.12840.37590.45780.03680.00030.6259-0.25330.409432.2257.8265.945
22.37540.1855-0.5532.4013-0.71260.3670.0211-0.0398-0.04910.1109-0.1364-0.1008-0.04090.04830.11530.49660.0177-0.0620.5107-0.02870.121650.1161.39369.117
30.132-0.096-0.0440.11860.04360.0317-0.0910.04-0.1162-0.0810.07070.11910.0160.02290.02030.7007-0.0556-0.12610.7451-0.08680.191951.04975.20489.448
42.6220.28670.43351.43771.19321.5966-0.4971-0.04110.5498-0.10190.14460.3348-0.12970.29970.35250.51050.0427-0.15950.5566-0.09160.206122.74648.151.233
50.2047-0.0544-0.180.76180.43740.4698-0.1205-0.12810.09470.02280.08880.02820.08990.09980.03170.49260.0491-0.0770.5653-0.0270.125324.07431.0244.859
60.291-0.27490.00072.3986-0.55470.1603-0.08320.06190.09210.04410.19370.2077-0.0005-0.0855-0.11050.556-0.0066-0.0650.57740.0610.13939.59631.57124.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2A22 - 42
3X-RAY DIFFRACTION2B10 - 15
4X-RAY DIFFRACTION3A43 - 50
5X-RAY DIFFRACTION3B1 - 9
6X-RAY DIFFRACTION4C1 - 21
7X-RAY DIFFRACTION5C22 - 42
8X-RAY DIFFRACTION5D10 - 15
9X-RAY DIFFRACTION6C43 - 50
10X-RAY DIFFRACTION6D1 - 9

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