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- PDB-6vwv: Transitional unit cell 2 of adenine riboswitch aptamer crystal ph... -

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Basic information

Entry
Database: PDB / ID: 6vwv
TitleTransitional unit cell 2 of adenine riboswitch aptamer crystal phase transition upon ligand binding
Componentsadenine riboswitch aptamer variant
KeywordsRNA / riboswitch / phase transition / time-resolved
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.
CitationJournal: Nat Commun / Year: 2021
Title: Synchronous RNA conformational changes trigger ordered phase transitions in crystals.
Authors: Ramakrishnan, S. / Stagno, J.R. / Conrad, C.E. / Ding, J. / Yu, P. / Bhandari, Y.R. / Lee, Y.T. / Pauly, G. / Yefanov, O. / Wiedorn, M.O. / Knoska, J. / Oberthur, D. / White, T.A. / Barty, A. ...Authors: Ramakrishnan, S. / Stagno, J.R. / Conrad, C.E. / Ding, J. / Yu, P. / Bhandari, Y.R. / Lee, Y.T. / Pauly, G. / Yefanov, O. / Wiedorn, M.O. / Knoska, J. / Oberthur, D. / White, T.A. / Barty, A. / Mariani, V. / Li, C. / Brehm, W. / Heinz, W.F. / Magidson, V. / Lockett, S. / Hunter, M.S. / Boutet, S. / Zatsepin, N.A. / Zuo, X. / Grant, T.D. / Pandey, S. / Schmidt, M. / Spence, J.C.H. / Chapman, H.N. / Wang, Y.X.
History
DepositionFeb 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: adenine riboswitch aptamer variant
B: adenine riboswitch aptamer variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7337
Polymers45,3752
Non-polymers3585
Water362
1
A: adenine riboswitch aptamer variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8864
Polymers22,6871
Non-polymers1993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: adenine riboswitch aptamer variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8473
Polymers22,6871
Non-polymers1592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.090, 25.490, 123.960
Angle α, β, γ (deg.)90.010, 84.050, 68.890
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain A
22chain B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GGCCchain AAA13 - 831 - 71
21GGCCchain BBB13 - 831 - 71
12ADEADEADEADEchain XAC101
22ADEADEADEADEchain YBF101

NCS ensembles :
ID
1
2

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Components

#1: RNA chain adenine riboswitch aptamer variant


Mass: 22687.383 Da / Num. of mol.: 2 / Mutation: variant / Source method: obtained synthetically / Source: (synth.) Vibrio vulnificus (bacteria) / References: GenBank: 675337566
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
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 / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.34 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 18, 2016 / Frequency: 120
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 3→27.53 Å / Num. obs: 7980 / % possible obs: 100 % / Redundancy: 118.1 % / Biso Wilson estimate: 75.2 Å2 / CC1/2: 0.9713 / CC star: 0.9927 / R split: 0.2343 / Net I/σ(I): 3.46
Reflection shellResolution: 3→3.11 Å / Redundancy: 74.6 % / Mean I/σ(I) obs: 0.57 / Num. unique obs: 812 / CC1/2: 0.4462 / CC star: 0.7855 / R split: 1.6994 / % possible all: 100
Serial crystallography measurementPulse duration: 43 fsec. / Pulse energy: 4.17 µJ / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: liquid injection / Method: injection
Serial crystallography sample delivery injectionDescription: GDVN / Filter size: 20 µm / Flow rate: 15 µL/min / Injector diameter: 75 µm
Serial crystallography data reductionCrystal hits: 12406 / Frames indexed: 3770 / Frames total: 250579

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Processing

Software
NameVersionClassification
PHENIX1.18rc5_3822refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tzx

4tzx


Resolution: 3→27 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 37.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 385 4.84 %
Rwork0.246 7567 -
obs0.2475 7952 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.91 Å2 / Biso mean: 75.0512 Å2 / Biso min: 35.93 Å2
Refinement stepCycle: final / Resolution: 3→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3006 23 2 3031
Biso mean--63.23 63.83 -
Num. residues----142
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1503X-RAY DIFFRACTIONPOSITIONAL0.027
12B1503X-RAY DIFFRACTIONPOSITIONAL0.027
21A10X-RAY DIFFRACTIONPOSITIONAL0.01
22B10X-RAY DIFFRACTIONPOSITIONAL0.01
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.110.4381440.391975780199
3.11-3.230.3626460.3256762808100
3.23-3.380.3261420.29370174399
3.38-3.560.3587460.2735790836100
3.56-3.780.2883400.282752792100
3.78-4.070.2518310.2557737768100
4.07-4.480.2441370.2398779816100
4.48-5.120.223330.2221781814100
5.12-6.440.2219300.2241750780100
6.44-270.2562360.2078758794100
Refinement TLS params.Method: refined / Origin x: -2.2 Å / Origin y: -12.062 Å / Origin z: 62.777 Å
111213212223313233
T0.3591 Å2-0.0002 Å20.0591 Å2-0.3936 Å2-0.0243 Å2--0.4769 Å2
L0.4806 °20.0056 °20.0526 °2-0.6484 °2-0.0194 °2---0.0781 °2
S0.1885 Å °-0.1165 Å °0.1012 Å °-0.0659 Å °0.0509 Å °-0.062 Å °-0.0802 Å °0.001 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )A13 - 83
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )A102
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )A201
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )A103
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )A101
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )B13 - 83
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )B201
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )B102
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:83 OR RESID 102:102 OR RESID 201:201 OR RESID 103:103 OR RESID 101:101 ) ) OR ( CHAIN B AND ( RESID 13:83 OR RESID 201:201 OR RESID 102:102 OR RESID 101:101 ) )B101

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