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- PDB-3e5f: Crystal Structures of the SMK box (SAM-III) Riboswitch with Se-SAM -

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Basic information

Entry
Database: PDB / ID: 3e5f
TitleCrystal Structures of the SMK box (SAM-III) Riboswitch with Se-SAM
ComponentsSMK box (SAM-III) Riboswitch for RNA
KeywordsRNA / SMK SAM riboswitch Shine-Delgarno translation regulation
Function / homologyChem-EEM / STRONTIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLu, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.
Authors: Lu, C. / Smith, A.M. / Fuchs, R.T. / Ding, F. / Rajashankar, K. / Henkin, T.M. / Ke, A.
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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 / struct_site
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_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_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_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

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Assembly

Deposited unit
A: SMK box (SAM-III) Riboswitch for RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,16317
Polymers17,4021
Non-polymers1,76116
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.776, 96.776, 86.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: RNA chain SMK box (SAM-III) Riboswitch for RNA


Mass: 17402.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The RNA is prepared by in vitro transcription
#2: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-EEM / [(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium / Se-ADENOSYLSELENOMETHIONINE


Mass: 446.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N6O5Se
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 mM sodium cacodylate, 80 mM SrCl, 15% MPD, 2 mM spermine-HCl, pH 7, vapor diffusion, hanging drop, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2MPD11
3spermine-HCl11
4sodium cacodylate12
5MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 5520 / % possible obs: 93.7 % / Observed criterion σ(I): 9.3 / Redundancy: 3.9 % / Biso Wilson estimate: 71.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.284 / % possible all: 74

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.7→19.79 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 1444146.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED, REFMAC WAS ALSO USED FOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.255 538 9.7 %RANDOM
Rwork0.227 ---
obs0.227 5519 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.7708 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 57.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.04 Å20 Å20 Å2
2---8.04 Å20 Å2
3---16.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1155 42 11 1208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.49
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 74 10.2 %
Rwork0.326 648 -
obs--75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ion.paramion.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3dna-rna_rep.paramwater.top
X-RAY DIFFRACTION4gtp.paramgtp.top
X-RAY DIFFRACTION5sesam.paramsesam.top

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