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- PDB-3npq: Structure of the S-adenosylhomocysteine riboswitch at 2.18 A -

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Basic information

Entry
Database: PDB / ID: 3npq
TitleStructure of the S-adenosylhomocysteine riboswitch at 2.18 A
ComponentsS-ADENOSYLHOMOCYSTEINE RIBOSWITCH
KeywordsRNA / riboswitch / S-adenosyl-homocysteine
Function / homologyCOBALT HEXAMMINE(III) / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10)
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1814 Å
AuthorsReyes, F.E. / Edwards, A.E. / Batey, R.T.
CitationJournal: Rna / Year: 2010
Title: Structural basis for recognition of S-adenosylhomocysteine by riboswitches.
Authors: Edwards, A.L. / Reyes, F.E. / Heroux, A. / Batey, R.T.
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-ADENOSYLHOMOCYSTEINE RIBOSWITCH
B: S-ADENOSYLHOMOCYSTEINE RIBOSWITCH
C: S-ADENOSYLHOMOCYSTEINE RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,03821
Polymers52,4693
Non-polymers3,57018
Water10,359575
1
A: S-ADENOSYLHOMOCYSTEINE RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6797
Polymers17,4901
Non-polymers1,1906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: S-ADENOSYLHOMOCYSTEINE RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6797
Polymers17,4901
Non-polymers1,1906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: S-ADENOSYLHOMOCYSTEINE RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6797
Polymers17,4901
Non-polymers1,1906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.793, 103.241, 69.583
Angle α, β, γ (deg.)90.00, 97.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-99-

HOH

21A-105-

HOH

31A-329-

HOH

41B-334-

HOH

51C-140-

HOH

61C-370-

HOH

71C-422-

HOH

81C-425-

HOH

91C-429-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:38 or resseq 43:54 ) and not element H
211chain B and (resseq 1:38 or resseq 43:54 ) and not element H
311chain C and (resseq 1:38 or resseq 43:54 ) and not element H

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Components

#1: RNA chain S-ADENOSYLHOMOCYSTEINE RIBOSWITCH


Mass: 17489.508 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Ralstonia solanacearum (bacteria)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 7
Details: 2.25 mM Spermine, 9 mM magnesium chloride, 0.9 mM spermidine, 2.5 mM Cobalt(III)hexammine chloride, 0.05 M sodium cacodylate pH 7.0, 5% (v/v) PEG 400, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: -1/2*h-1/2*k-l,-1/2*h-1/2*k+l,-1/2*h+1/2*k / Fraction: 0.53
ReflectionResolution: 1.95→23.014 Å / Num. obs: 41336 / % possible obs: 86.4 % / Redundancy: 6.2 % / Rsym value: 0.071
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.0541.1571.0050.71300632680.5661.1571.0051.447
2.05-2.184.30.7350.6451.11960045950.3470.7350.6452.269.8
2.18-2.3350.4640.4151.82785855730.2030.4640.4153.790.5
2.33-2.516.70.2750.2542.93887757640.1050.2750.2546.799.7
2.51-2.7570.1510.145.23735953150.0560.1510.141199.8
2.75-3.087.10.0860.0797.13421547960.0320.0860.07917.899.9
3.08-3.567.10.0670.0628.73031542530.0250.0670.06225.599.8
3.56-4.3670.0590.05510.62528135880.0220.0590.0552999.2
4.36-6.166.80.0630.058101846727340.0240.0630.05830.298.3
6.16-23.0146.40.0570.05211.3934614500.0220.0570.05231.193.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.93 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.01 Å
Translation2.5 Å23.01 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASERphasing
PHENIX1.4_87refinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NPN

3npn


Resolution: 2.1814→23.014 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0.03 / Phase error: 28.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2454 1761 5.38 %
Rwork0.2353 --
obs0.2358 32745 95.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.228 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.1324 Å20 Å20.2297 Å2
2--5.5823 Å20 Å2
3---0.646 Å2
Refinement stepCycle: LAST / Resolution: 2.1814→23.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3235 183 575 3993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013793
X-RAY DIFFRACTIONf_angle_d0.5365981
X-RAY DIFFRACTIONf_dihedral_angle_d18.421482
X-RAY DIFFRACTIONf_chiral_restr0.033765
X-RAY DIFFRACTIONf_plane_restr0.001156
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1056X-RAY DIFFRACTIONPOSITIONAL
12B1056X-RAY DIFFRACTIONPOSITIONAL0.004
13C1058X-RAY DIFFRACTIONPOSITIONAL0.017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1814-2.25160.53861200.38962348X-RAY DIFFRACTION77
2.2516-2.33190.33781340.38082579X-RAY DIFFRACTION84
2.3319-2.4250.39571470.38462817X-RAY DIFFRACTION92
2.425-2.53510.30671470.34782889X-RAY DIFFRACTION93
2.5351-2.66820.35331490.35292905X-RAY DIFFRACTION94
2.6682-2.83470.27281490.30862899X-RAY DIFFRACTION94
2.8347-3.05250.29041530.25442926X-RAY DIFFRACTION94
3.0525-3.35750.21641430.21462943X-RAY DIFFRACTION95
3.3575-3.83860.19591470.19452944X-RAY DIFFRACTION95
3.8386-4.81830.19051490.1872920X-RAY DIFFRACTION94
4.8183-17.11420.22351490.18362917X-RAY DIFFRACTION92
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)
10.28170.1603-0.40810.08750.13452.2812-0.3050.143-0.04510.0207-0.19580.05410.033-0.46230.32330.1388-0.03050.01150.4242-0.07970.184829.0998-18.06214.871
20.5523-0.5206-0.18590.60170.26320.43130.2202-0.0059-0.0422-0.2975-0.09130.10540.05270.0813-0.09290.35550.0495-0.03010.1851-0.00810.196632.611913.702611.0305
30.52140.52710.5161.27640.46710.5746-0.18170.27810.19960.02690.13230.17450.03460.23020.02480.1032-0.0222-0.00570.18780.06780.195813.06922.915334.7951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and not element H
2X-RAY DIFFRACTION2chain B and not element H
3X-RAY DIFFRACTION3chain C and not element H

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