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- PDB-6c27: SAM-III riboswitch ON-state -

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Basic information

Entry
Database: PDB / ID: 6c27
TitleSAM-III riboswitch ON-state
ComponentsSAM-III riboswitch
KeywordsRNA / riboswitch / regulation
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.601 Å
AuthorsGrigg, J.C. / Price, I.R. / Ke, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-086766 United States
CitationJournal: To Be Published
Title: Evidence for two-tiered conformation selection in the SAM-III riboswitch
Authors: Price, I.R. / Grigg, J.C. / Martell, D.J. / Ding, F. / Peng, C. / Ke, A.
History
DepositionJan 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: SAM-III riboswitch
B: SAM-III riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,99710
Polymers30,7082
Non-polymers1,2898
Water00
1
A: SAM-III riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9995
Polymers15,3541
Non-polymers6444
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SAM-III riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9995
Polymers15,3541
Non-polymers6444
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.011, 96.791, 168.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GTP / Beg label comp-ID: GTP / End auth comp-ID: C / End label comp-ID: C / Auth seq-ID: 1 - 47 / Label seq-ID: 1 - 47

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: RNA chain SAM-III riboswitch


Mass: 15354.081 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription from a modified pUC19 vector with T7 RNA polymerase
Source: (synth.) Enterococcus faecalis (bacteria)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CoH18N6

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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: 4.92 Å3/Da / Density % sol: 75.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM MgCl2, 50 mM sodium cacodylate pH 7.0, 1 mM hexamine cobalt chloride, 2 mM spermine, and 12-16 % (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 6980 / % possible obs: 94.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 122.49 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.018 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.6-3.664.60.4492540.592173.8
3.66-3.734.70.3352750.615176.2
3.73-3.85.40.2142800.604176.9
3.8-3.885.60.1973100.637185.9
3.88-3.965.80.1953160.659189.3
3.96-4.055.90.2523660.597195.8
4.05-4.166.30.3023510.574199.2
4.16-4.276.60.2493570.643199.2
4.27-4.396.60.2433730.6461100
4.39-4.546.80.1923560.6831100
4.54-4.76.70.1433830.7251100
4.7-4.896.80.1153440.781100
4.89-5.116.80.1073850.8311100
5.11-5.386.70.0923601.0441100
5.38-5.716.60.0853721.3321100
5.71-6.156.50.0843801.558199.7
6.15-6.776.30.0683731.8611100
6.77-7.756.10.0463711.8191100
7.75-9.7560.0353861.8251100
9.75-505.70.0253881.646192.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
SOLVEphasing
PDB_EXTRACT3.24data extraction
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.601→37.005 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.39
RfactorNum. reflection% reflection
Rfree0.2432 318 4.68 %
Rwork0.2103 --
obs0.2117 6800 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 431.26 Å2 / Biso mean: 180.3013 Å2 / Biso min: 83.48 Å2
Refinement stepCycle: final / Resolution: 3.601→37.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2036 56 0 2092
Biso mean--197.51 --
Num. residues----94
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012324
X-RAY DIFFRACTIONf_angle_d0.3793666
X-RAY DIFFRACTIONf_chiral_restr0.015468
X-RAY DIFFRACTIONf_plane_restr0.00194
X-RAY DIFFRACTIONf_dihedral_angle_d10.9291126
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A874X-RAY DIFFRACTION0.317TORSIONAL
12B874X-RAY DIFFRACTION0.317TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6005-3.660.33461430.30612974311787
4.535-37.00740.2231750.18813508368399
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)
12.6161.58310.01910.99190.13480.1653-0.71023.09052.3015-0.96330.94321.24071.30951.9655-0.01281.5874-0.4379-0.17032.62670.16811.2731-11.2082-11.852-34.1717
20.527-0.1865-0.29670.15160.48820.5928-0.0208-0.3661-0.0891.0884-0.50320.9846-2.04780.7183-0.00051.6776-0.1373-0.10421.1068-0.05221.6162-3.48088.3761-31.7161
3-0.61170.1240.0985-0.26380.4231-0.4127-0.51070.00680.1184-0.1159-0.10380.2414-0.77720.0816-01.50970.02470.01380.9872-0.20491.2706-1.83657.4738-16.8439
40.0302-0.11250.09071.0424-0.21331.4009-0.14860.19760.78892.09180.26180.99220.76160.0421-0.54151.1869-0.69370.36471.17220.06281.6256-13.3741-17.6317-31.8322
50.6348-0.1549-0.34790.0831-0.62750.6732-0.3171-0.48350.67561.32321.0245-1.7137-0.78990.42840.05641.40630.529-0.09561.69960.18161.589620.4231-4.936931.7802
60.25790.048-0.04110.04980.30530.36740.45410.52851.7476-0.38550.9096-0.8104-2.74140.10610.01991.39370.161-0.21661.72270.00651.836212.492216.36729.3279
7-1.11080.28121.46821.26790.6298-0.7003-0.27580.04120.2131-0.5550.2777-0.70760.4197-0.08230.00021.15920.25590.09651.54070.02931.354914.3912.744419.1324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 8 )A2 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 17 )A9 - 17
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 39 )A18 - 39
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 47 )A40 - 47
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 10 )B2 - 10
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 19 )B11 - 19
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 47 )B20 - 47

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