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- PDB-3v7e: Crystal structure of YbxF bound to the SAM-I riboswitch aptamer -

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Basic information

Entry
Database: PDB / ID: 3v7e
TitleCrystal structure of YbxF bound to the SAM-I riboswitch aptamer
Components
  • Ribosome-associated protein L7Ae-like
  • SAM-I riboswitch aptamer with an engineered helix P3
KeywordsRIBOSOMAL PROTEIN/RNA / RNA-protein complex / riboswitch / K-turn / L7Ae-like / A member of the L7Ae/L30e superfamily / Unknown function / K-turn motif / RIBOSOMAL PROTEIN-RNA complex
Function / homology
Function and homology information


ribosome / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, putative / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COBALT HEXAMMINE(III) / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA-binding protein YbxF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBaird, N.J. / Zhang, J. / Hamma, T. / Ferre-D'Amare, A.R.
CitationJournal: Rna / Year: 2012
Title: YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.
Authors: Baird, N.J. / Zhang, J. / Hamma, T. / Ferre-D'Amare, A.R.
History
DepositionDec 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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: Ribosome-associated protein L7Ae-like
B: Ribosome-associated protein L7Ae-like
C: SAM-I riboswitch aptamer with an engineered helix P3
D: SAM-I riboswitch aptamer with an engineered helix P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,63046
Polymers98,3984
Non-polymers4,23242
Water27015
1
A: Ribosome-associated protein L7Ae-like
C: SAM-I riboswitch aptamer with an engineered helix P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,84728
Polymers49,1992
Non-polymers2,64826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-87 kcal/mol
Surface area23570 Å2
MethodPISA
2
B: Ribosome-associated protein L7Ae-like
D: SAM-I riboswitch aptamer with an engineered helix P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,78318
Polymers49,1992
Non-polymers1,58416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-78 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.762, 54.305, 106.366
Angle α, β, γ (deg.)90.00, 116.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein Ribosome-associated protein L7Ae-like


Mass: 8398.870 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU01090, rplGB, ybaB, ybxF / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: P46350
#2: RNA chain SAM-I riboswitch aptamer with an engineered helix P3


Mass: 40800.328 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)

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Non-polymers , 4 types, 57 molecules

#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 150 M RNA, 210 M YbxF, 10 mM MgCl2, 10 mM SAM, 40 mM KCl, 20 mM HEPES-KOH, 1 mM spermine, 1 mM cobalt hexammine, and 1 mM DTT, 100 mM potassium cacodylate pH 6.0, 200 mM MgCl2 and 25% (v/v) ...Details: 150 M RNA, 210 M YbxF, 10 mM MgCl2, 10 mM SAM, 40 mM KCl, 20 mM HEPES-KOH, 1 mM spermine, 1 mM cobalt hexammine, and 1 mM DTT, 100 mM potassium cacodylate pH 6.0, 200 mM MgCl2 and 25% (v/v) PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2011
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 25202 / Num. obs: 22926 / Observed criterion σ(I): 116.2 / Redundancy: 4.3 % / Biso Wilson estimate: 121.2 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 25.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.46 / Num. unique all: 2244 / % possible all: 92.7

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Processing

Software
NameVersionClassification
ALSBOSdata collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: M. jannaschii L7Ae protein (PDB ID 1SDS, chain A)

1sds


Resolution: 2.8→29.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 74723.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2276 9.9 %RANDOM
Rwork0.218 ---
obs0.218 22926 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.0533 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 75.6 Å2
Baniso -1Baniso -2Baniso -3
1-25.12 Å20 Å215.88 Å2
2--7.19 Å20 Å2
3----32.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 5372 202 15 6551
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.521.5
X-RAY DIFFRACTIONc_mcangle_it5.582
X-RAY DIFFRACTIONc_scbond_it4.992
X-RAY DIFFRACTIONc_scangle_it6.872.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.451 320 10 %
Rwork0.404 2870 -
obs--78.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6sam.parsam.top
X-RAY DIFFRACTION7nco.parnco.top

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