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- PDB-5swd: Structure of the adenine riboswitch aptamer domain in an intermed... -

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Entry
Database: PDB / ID: 5swd
TitleStructure of the adenine riboswitch aptamer domain in an intermediate-bound state
ComponentsVibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain
KeywordsRNA / adenine riboswitch / purine riboswitch / ligand mixing / intermediate state / 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: 2.5 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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 / _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.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.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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 4, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,5836
Polymers45,3752
Non-polymers2084
Water27015
1
A: Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8714
Polymers22,6871
Non-polymers1843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7122
Polymers22,6871
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.910, 46.720, 92.250
Angle α, β, γ (deg.)90.000, 94.060, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: A / End label comp-ID: A / Refine code: 0 / Auth seq-ID: 13 - 76 / Label seq-ID: 1 - 64

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2 / 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: 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: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
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: 2.5→31.06 Å / Num. obs: 14357 / % possible obs: 100 % / Redundancy: 346.8 % / Biso Wilson estimate: 80.9 Å2 / R split: 0.141 / Net I/σ(I): 3.49
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 188.3 % / Num. unique all: 1431 / R split: 0.8684 / % possible all: 100

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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: 5.0E+54 / Resolution: 2.5→30.92 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.2579 / WRfactor Rwork: 0.2176 / FOM work R set: 0.6535 / SU B: 38.407 / SU ML: 0.342 / SU R Cruickshank DPI: 0.6685 / SU Rfree: 0.2762 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.669 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 768 5.5 %RANDOM
Rwork0.1949 ---
obs0.1969 13212 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 219.21 Å2 / Biso mean: 90.59 Å2 / Biso min: 46.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å2-0.58 Å2
2--2.41 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 2.5→30.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2826 13 15 2854
Biso mean--85.09 70.49 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0113218
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.2895012
X-RAY DIFFRACTIONr_chiral_restr0.1010.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021391
X-RAY DIFFRACTIONr_scbond_it5.2727.0643218
Refine LS restraints NCS

Ens-ID: 1 / Number: 3441 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.735 44 -
Rwork0.548 735 -
all-779 -
obs--73.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0175-0.0517-0.61031.36550.41111.14230.08410.55860.4289-0.296-0.10550.104-0.2571-0.11250.02140.09410.0387-0.02690.14130.07570.1033-2.7437-0.012128.5524
23.3817-0.1576-0.27331.4932-0.33290.86620.00450.7867-0.4591-0.3224-0.01860.01520.0843-0.04180.01420.07460.0071-0.00780.2179-0.11530.08487.0972-21.249323.2953
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 77
2X-RAY DIFFRACTION2B13 - 80

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