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- PDB-6vmy: Structure of the B. subtilis cobalamin riboswitch -

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Basic information

Entry
Database: PDB / ID: 6vmy
TitleStructure of the B. subtilis cobalamin riboswitch
ComponentsB. subtilis cobalamin riboswitch
KeywordsRNA / riboswitch / cobalamin / gene regulation
Function / homologyAdenosylcobalamin / COBALT HEXAMMINE(III) / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.25 Å
AuthorsChan, C.W. / Mondragon, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM058443 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118108 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008382 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding.
Authors: Chan, C.W. / Mondragon, A.
History
DepositionJan 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: B. subtilis cobalamin riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,05321
Polymers48,0531
Non-polymers3,00020
Water86548
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.282, 118.282, 261.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: RNA chain B. subtilis cobalamin riboswitch


Mass: 48052.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Details (production host): RNA was produced by in vitro transcription using T7 RNA polymerase. The recombinant T7 polymerase was purified from E. coli.
Production host: Escherichia coli K-12 (bacteria) / References: GenBank: CP046047.1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-B1Z / Adenosylcobalamin / Cobamamide


Mass: 1580.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C72H101CoN18O17P / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.51 Å3/Da / Density % sol: 77.69 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: Purified RNA was incubated at room temperature for 30 minutes in 25 mM Tris-HCl, pH 8.0, 50 mM potassium chloride, 10 mM magnesium chloride, 0.5 mM adenosylcobalamin prior to crystallization ...Details: Purified RNA was incubated at room temperature for 30 minutes in 25 mM Tris-HCl, pH 8.0, 50 mM potassium chloride, 10 mM magnesium chloride, 0.5 mM adenosylcobalamin prior to crystallization in 50 mM sodium cacodylate, 15% (v/v) PEG 400, 0.2 mM cobalt hexamine, 80 mM magnesium acetate, 1 mM spermine between pH 6.0 to pH 6.5 at 14C by vapor diffusion in a hanging drop format
PH range: 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 3, 2013 / Details: Mirrors
RadiationMonochromator: Kohzu monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.253→39.213 Å / Num. obs: 15338 / % possible obs: 92.8 % / Redundancy: 47 % / CC1/2: 0.996 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.025 / Rrim(I) all: 0.162 / Net I/σ(I): 18.2
Reflection shellResolution: 3.28→3.46 Å / Redundancy: 54 % / Rmerge(I) obs: 4.129 / Num. unique obs: 41046 / CC1/2: 0.598 / Rpim(I) all: 0.561 / Rrim(I) all: 4.168 / % possible all: 43.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
Cootmodel building
RefinementMethod to determine structure: MIRAS / Resolution: 3.25→39.21 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: FREE R-VALUE / ESU R: 1.731 / ESU R Free: 0.47
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.279 785 5.118 %
Rwork0.263 --
obs-15338 86.3 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 129.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.693 Å20.347 Å20 Å2
2--0.693 Å20 Å2
3----2.248 Å2
Refinement stepCycle: LAST / Resolution: 3.25→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3174 179 48 3401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0113776
X-RAY DIFFRACTIONr_bond_other_d0.0010.0191681
X-RAY DIFFRACTIONr_angle_refined_deg0.8071.3735974
X-RAY DIFFRACTIONr_angle_other_deg2.16533993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0135.0731374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.7365116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0330.0342509
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02832
X-RAY DIFFRACTIONr_nbd_refined0.1480.2587
X-RAY DIFFRACTIONr_nbd_other0.220.275
X-RAY DIFFRACTIONr_nbtor_refined0.2530.21257
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.260
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_it1.84713.6553776
X-RAY DIFFRACTIONr_scbond_other1.84713.6553771
X-RAY DIFFRACTIONr_scangle_it3.11720.5395974
X-RAY DIFFRACTIONr_scangle_other3.11820.5395965
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.34 Å
RfactorNum. reflection% reflection
Rfree0.612 4 -
Rwork0.376 124 -
obs--9.99 %

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