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- PDB-2xnw: XPT-PBUX C74U RIBOSWITCH FROM B. SUBTILIS BOUND TO A TRIAZOLO- TR... -

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Basic information

Entry
Database: PDB / ID: 2xnw
TitleXPT-PBUX C74U RIBOSWITCH FROM B. SUBTILIS BOUND TO A TRIAZOLO- TRIAZOLE-DIAMINE LIGAND IDENTIFIED BY VIRTUAL SCREENING
ComponentsGUANINE RIBOSWITCH
KeywordsRNA
Function / homologyACETATE ION / : / COBALT HEXAMMINE(III) / Chem-ZZR / RNA / RNA (> 10)
Function and homology information
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDaldrop, P. / Reyes, F.E. / Robinson, D.A. / Hammond, C.M. / Lilley, D.M.J. / Brenk, R.
CitationJournal: Chem. Biol. / Year: 2011
Title: Novel ligands for a purine riboswitch discovered by RNA-ligand docking.
Authors: Daldrop, P. / Reyes, F.E. / Robinson, D.A. / Hammond, C.M. / Lilley, D.M. / Batey, R.T. / Brenk, R.
History
DepositionAug 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.2Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _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: GUANINE RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,87411
Polymers21,5081
Non-polymers1,36610
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.895, 35.380, 42.197
Angle α, β, γ (deg.)90.00, 92.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain GUANINE RIBOSWITCH


Mass: 21507.768 Da / Num. of mol.: 1 / Fragment: APTAMER DOMAIN, RESIDUES 15-81 / Source method: obtained synthetically / Source: (synth.) BACILLUS SUBTILIS (bacteria)

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Non-polymers , 5 types, 339 molecules

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


Mass: 161.116 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZZR / 3,6-diamino-1,5-dihydro[1,2,4]triazolo[4,3-b][1,2,4]triazol-4-ium


Mass: 140.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6N7
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5
Details: 22.5% PEG 4000, 10MM K-HEPES PH 7.5, 12MM COBALT HEXAMMINE, 560MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93344
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93344 Å / Relative weight: 1
ReflectionResolution: 1.5→67.88 Å / Num. obs: 30250 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G9C

2g9c


Resolution: 1.5→67.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.935 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24412 1527 5.1 %RANDOM
Rwork0.21348 ---
obs0.21509 28631 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å2-0.78 Å2
2---1.51 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→67.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1366 64 329 1759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211575
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.68632471
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02672
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it0.9011.53
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59222
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.45331572
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9274.52469
X-RAY DIFFRACTIONr_scangle_other
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: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 125 -
Rwork0.335 2156 -
obs--95.44 %

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