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- PDB-5swe: Ligand-bound structure of adenine riboswitch aptamer domain conve... -

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Entry
Database: PDB / ID: 5swe
TitleLigand-bound structure of adenine riboswitch aptamer domain converted in crystal from its ligand-free state using ligand mixing serial femtosecond crystallography
ComponentsVibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain
KeywordsRNA / adenine riboswitch / purine riboswitch / ligand mixing / gene regulation / X-ray free electron laser
Function / homologyADENINE / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStagno, J.R. / Wang, Y.-X. / Liu, Y. / Bhandari, Y.R. / Conrad, C.E. / Nelson, G. / Li, C. / Wendel, D.R. / White, T.A. / Barty, A. ...Stagno, J.R. / Wang, Y.-X. / Liu, Y. / Bhandari, Y.R. / Conrad, C.E. / Nelson, G. / Li, C. / Wendel, D.R. / White, T.A. / Barty, A. / Tuckey, R.A. / Zatsepin, N.A. / Grant, T.D. / Fromme, P. / Tan, K. / Ji, X. / Spence, J.C.H.
CitationJournal: Nature / Year: 2017
Title: Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.
Authors: Stagno, J.R. / Liu, Y. / Bhandari, Y.R. / Conrad, C.E. / Panja, S. / Swain, M. / Fan, L. / Nelson, G. / Li, C. / Wendel, D.R. / White, T.A. / Coe, J.D. / Wiedorn, M.O. / Knoska, J. / ...Authors: Stagno, J.R. / Liu, Y. / Bhandari, Y.R. / Conrad, C.E. / Panja, S. / Swain, M. / Fan, L. / Nelson, G. / Li, C. / Wendel, D.R. / White, T.A. / Coe, J.D. / Wiedorn, M.O. / Knoska, J. / Oberthuer, D. / Tuckey, R.A. / Yu, P. / Dyba, M. / Tarasov, S.G. / Weierstall, U. / Grant, T.D. / Schwieters, C.D. / Zhang, J. / Ferre-D'Amare, A.R. / Fromme, P. / Draper, D.E. / Liang, M. / Hunter, M.S. / Boutet, S. / Tan, K. / Zuo, X. / Ji, X. / Barty, A. / Zatsepin, N.A. / Chapman, H.N. / Spence, J.C. / Woodson, S.A. / Wang, Y.X.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Data collection / Database references
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_R_split / _reflns_shell.pdbx_R_split
Revision 1.3Feb 14, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 4, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8232
Polymers22,6871
Non-polymers1351
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.900, 154.900, 25.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain


Mass: 22687.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio vulnificus (bacteria)
#2: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5

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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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 6.5
Details: 40 mM sodium cacodylate, pH 6.5, 80 mM potassium chloride, 100 mM magnesium chloride, 12 mM spermine tetrahydrochloride, 65% v/v (+/-)-2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 14, 2016
RadiationMonochromator: KB mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3→26.32 Å / Num. obs: 4115 / % possible obs: 95 % / Redundancy: 20.3 % / Biso Wilson estimate: 66.4 Å2 / R split: 0.6689 / Net I/σ(I): 1.37
Reflection shellResolution: 3→3.31 Å / Redundancy: 13 % / Num. unique all: 945 / R split: 1.0157 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZX

4tzx


Resolution: 3→26.32 Å / Cor.coef. Fo:Fc: 0.836 / Cor.coef. Fo:Fc free: 0.718 / WRfactor Rfree: 0.2579 / WRfactor Rwork: 0.2176 / FOM work R set: 0.6535 / SU B: 79.047 / SU ML: 1.489 / SU R Cruickshank DPI: 0.6685 / SU Rfree: 0.2762 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.73 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.379 196 4.8 %RANDOM
Rwork0.3489 ---
obs0.3503 3919 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.85 Å2 / Biso mean: 58.062 Å2 / Biso min: 30.14 Å2
Baniso -1Baniso -2Baniso -3
1-4.32 Å20 Å2-0 Å2
2---2.91 Å20 Å2
3----1.41 Å2
Refinement stepCycle: final / Resolution: 3→26.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1502 10 0 1512
Biso mean--63.22 --
Num. residues----71
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0111688
X-RAY DIFFRACTIONr_angle_refined_deg0.8561.3022623
X-RAY DIFFRACTIONr_chiral_restr0.070.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02731
X-RAY DIFFRACTIONr_scbond_it1.915.8041688
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 7 -
Rwork0.421 230 -
all-237 -
obs--75.72 %

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