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- PDB-2yif: Crystal structure of a F. nucleatum FMN riboswitch - Free state -

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Basic information

Entry
Database: PDB / ID: 2yif
TitleCrystal structure of a F. nucleatum FMN riboswitch - Free state
Components(FMN RIBOSWITCH) x 2
KeywordsRNA / TRANSLATION
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.298 Å
AuthorsVicens, Q. / Mondragon, E. / Batey, R.T.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Molecular Sensing by the Aptamer Domain of the Fmn Riboswitch: A General Model for Ligand Binding by Conformational Selection.
Authors: Vicens, Q. / Mondragon, E. / Batey, R.T.
History
DepositionMay 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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
X: FMN RIBOSWITCH
Z: FMN RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,60616
Polymers36,2362
Non-polymers37014
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-83 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.472, 73.472, 135.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain FMN RIBOSWITCH /


Mass: 17575.324 Da / Num. of mol.: 1 / Fragment: APTAMER DOMAIN, RESIDUES 2495-2544 / Mutation: YES / Source method: obtained synthetically
Source: (synth.) FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM (bacteria)
References: GenBank: 20095250
#2: RNA chain FMN RIBOSWITCH /


Mass: 18661.000 Da / Num. of mol.: 1 / Fragment: APTAMER DOMAIN, RESIDUES 2550-2601 / Mutation: YES / Source method: obtained synthetically
Source: (synth.) FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM (bacteria)
References: GenBank: 20095250
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.91 Å3/Da / Density % sol: 64.3 % / Description: NONE
Crystal growDetails: RNA WAS CRYSTALLIZED FROM 11% PEG-4000, 0.32 M MGCL2, AND 0.01 M TRIS-CL, PH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 6627 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 113.49 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.9
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F2Q

3f2q


Resolution: 3.298→29.844 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 26.19 / Stereochemistry target values: ML
Details: U54 AND PHOSPHATE GROUPS OF THE GTP IN CHAINS X, Z ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2572 356 5.6 %
Rwork0.2058 --
obs0.2087 6383 94.52 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.233 e/Å3
Displacement parametersBiso mean: 132.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.4284 Å20 Å20 Å2
2---5.4284 Å20 Å2
3---9.2468 Å2
Refinement stepCycle: LAST / Resolution: 3.298→29.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2374 14 26 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022683
X-RAY DIFFRACTIONf_angle_d0.5174201
X-RAY DIFFRACTIONf_dihedral_angle_d16.8981350
X-RAY DIFFRACTIONf_chiral_restr0.053540
X-RAY DIFFRACTIONf_plane_restr0.036114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.298-4.15340.29841690.26372799X-RAY DIFFRACTION90
4.1534-29.84550.24421870.18873228X-RAY DIFFRACTION99

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