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- PDB-6yl5: Crystal structure of the SAM-SAH riboswitch with SAH -

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Basic information

Entry
Database: PDB / ID: 6yl5
TitleCrystal structure of the SAM-SAH riboswitch with SAH
ComponentsChains: A,B,C,D,E,F,G,H,I,J,K,L
KeywordsRNA / Pseudoknot / SAM / Riboswitch
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10)
Function and homology information
Biological speciesRoseobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
Ministry of Education (MoE, China) China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure and ligand-induced folding of the SAM/SAH riboswitch.
Authors: Huang, L. / Liao, T.W. / Wang, J. / Ha, T. / Lilley, D.M.J.
History
DepositionApr 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chains: A,B,C,D,E,F,G,H,I,J,K,L
B: Chains: A,B,C,D,E,F,G,H,I,J,K,L
C: Chains: A,B,C,D,E,F,G,H,I,J,K,L
D: Chains: A,B,C,D,E,F,G,H,I,J,K,L
E: Chains: A,B,C,D,E,F,G,H,I,J,K,L
F: Chains: A,B,C,D,E,F,G,H,I,J,K,L
G: Chains: A,B,C,D,E,F,G,H,I,J,K,L
H: Chains: A,B,C,D,E,F,G,H,I,J,K,L
I: Chains: A,B,C,D,E,F,G,H,I,J,K,L
J: Chains: A,B,C,D,E,F,G,H,I,J,K,L
K: Chains: A,B,C,D,E,F,G,H,I,J,K,L
L: Chains: A,B,C,D,E,F,G,H,I,J,K,L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,15943
Polymers135,96712
Non-polymers4,19131
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-155 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.750, 147.610, 74.660
Angle α, β, γ (deg.)90.000, 92.070, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-231-

HOH

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Components

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RNA chain , 1 types, 12 molecules ABCDEFGHIJKL

#1: RNA chain
Chains: A,B,C,D,E,F,G,H,I,J,K,L


Mass: 11330.620 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)

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Non-polymers , 5 types, 564 molecules

#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.66 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.01 M Magnesium Sulfate, 0.05 M Sodium Cacodylate pH 6.0, 1.8 M Lithium Sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.912 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.7→74.75 Å / Num. obs: 190284 / % possible obs: 98.4 % / Redundancy: 3.39 % / Biso Wilson estimate: 34.22 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.057 / Net I/σ(I): 7.3
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4855 / CC1/2: 0.5 / Rpim(I) all: 0.586

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→74.61 Å / SU ML: 0.2066 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1816
RfactorNum. reflection% reflection
Rfree0.2004 9346 4.91 %
Rwork0.1723 --
obs0.1736 190284 94.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4452 247 533 5232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01195211
X-RAY DIFFRACTIONf_angle_d1.90068079
X-RAY DIFFRACTIONf_chiral_restr0.07481074
X-RAY DIFFRACTIONf_plane_restr0.0189225
X-RAY DIFFRACTIONf_dihedral_angle_d15.89892583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.37053180.33845687X-RAY DIFFRACTION89.98
1.72-1.740.36272910.3266235X-RAY DIFFRACTION96.21
1.74-1.760.282590.30126215X-RAY DIFFRACTION96.21
1.76-1.790.33052690.29566274X-RAY DIFFRACTION96.59
1.79-1.810.27433220.27476154X-RAY DIFFRACTION96.83
1.81-1.840.25743190.26266168X-RAY DIFFRACTION96.55
1.84-1.860.26993470.25866215X-RAY DIFFRACTION96.15
1.86-1.890.28523610.27025828X-RAY DIFFRACTION92.69
1.89-1.920.31262990.27435792X-RAY DIFFRACTION89.75
1.92-1.950.24173250.24186106X-RAY DIFFRACTION95.46
1.95-1.980.21853880.22336137X-RAY DIFFRACTION97.17
1.98-2.020.25733710.22836080X-RAY DIFFRACTION94.88
2.02-2.060.23493980.22585749X-RAY DIFFRACTION91.41
2.06-2.10.24763400.21336087X-RAY DIFFRACTION95.81
2.1-2.150.26543340.2066203X-RAY DIFFRACTION96.53
2.15-2.20.26273350.20086206X-RAY DIFFRACTION96.32
2.2-2.250.25833260.20545944X-RAY DIFFRACTION92.78
2.25-2.310.24073400.2026133X-RAY DIFFRACTION96.73
2.31-2.380.22923330.19976173X-RAY DIFFRACTION95.73
2.38-2.460.21593000.19156043X-RAY DIFFRACTION94.71
2.46-2.540.24412710.19326273X-RAY DIFFRACTION96.72
2.54-2.650.24162790.19486001X-RAY DIFFRACTION93.58
2.65-2.770.23093550.19826012X-RAY DIFFRACTION93.58
2.77-2.910.22652630.19715956X-RAY DIFFRACTION93.34
2.91-3.10.21922510.17186050X-RAY DIFFRACTION92.69
3.1-3.330.15562810.1595920X-RAY DIFFRACTION92.26
3.33-3.670.16131990.14025882X-RAY DIFFRACTION90.13
3.67-4.20.15552170.12585845X-RAY DIFFRACTION89.91
4.2-5.290.15283020.12995884X-RAY DIFFRACTION91.24
5.29-74.610.16273530.14255686X-RAY DIFFRACTION89.45
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.26860940043.084956953570.7932909126052.992671805540.9266337090877.88938663549-0.565162599221-0.727797738330.6348948216460.03705274539470.2236923823280.734861931731-0.169517045601-0.6882277516640.2859916079530.398564448882-0.0297530411533-0.08441699932080.361216666257-0.00439901323720.51713400068519.727889918611.46303685524.960682496
24.762795791060.4737649183431.490657733380.510130010807-0.266231529042.48461290560.0678485225926-0.0693616225681-0.0472421268419-0.0875276597830.01948103910790.05020715958040.111542049665-0.019135885974-0.0370199173450.313678040836-0.00477246602122-0.0002658415465180.2596084361970.02732187519870.28238403653738.891563895315.002091381424.2703098182
31.795507677151.57390699642-0.2400418324457.03747929359-0.9658440281884.44856697408-0.3924993719250.3367182597230.255625651797-0.8378003498910.4650969470241.023262530450.342524785588-0.337581455051-0.08318013097590.369138577838-0.0113377522383-0.1835618624390.383592811570.07012877059630.53786961058119.06520629736.0600998636219.2185913275
40.743433133656-0.5521415608050.6226143213811.38669973956-0.05774630194381.79907652856-0.03318722402620.09200083328240.2611614665690.0120633476703-0.0991354791134-0.0897883586696-0.2939995676140.365117051730.1418098330290.36433250102-0.0529994895291-0.01057138483660.3888839269840.02599950908450.31929052467645.0959805123.309765512227.4329442297
54.726685782031.375269483072.196184614521.18955507668-0.283280492811.17737153634-0.4460633981660.4766067924830.744977846508-0.313708967944-0.0283143068183-0.419872005751-0.1553557516620.1155260722160.4404953006710.37821642686-0.1086692676820.03797646955480.6402054367860.01533255000420.68555502744-4.725533292624.30588530811.5396352546
64.116128682132.801437757950.9002407031169.420738631826.164167984564.55146894658-0.4537559284320.1026073410870.0410077414431-1.189739757930.38563776418-0.0506776251385-0.5471102726140.956770372907-0.01392658303320.490695391611-0.0984668406450.06044939591790.314189543525-0.004832342434650.352282203764-18.2959726937-2.027939519517.60976787802
72.200714267840.7641551855780.3821489416711.32888095109-0.7297214338511.1086036817-0.735396287370.9670042650870.356443710234-0.2636297787860.52753812525-0.884162964525-0.3467829153520.3162649831020.2672781863020.483243777897-0.210274401296-0.003722997216290.7260808903460.01441995438490.7768531916420.0658822954587.1337834966812.6580481892
82.576953993262.496698759871.53569596214.632253719570.6696955689866.51309370586-0.0619040251243-0.0474213744326-0.162988522677-0.3640120711630.20145162502-0.627217367150.2855700639620.238921015956-0.2274970495090.3779884196870.004325560476410.08925242407210.340161076714-0.08539182115620.379348136277-14.3406450359-10.523670472211.1405120559
96.40337005996-4.392069578810.4956120708553.59734037359-0.4241100187551.054489775-0.3315353733870.00220758476126-0.3354384642390.3405910049980.2662844204730.07871515516810.05057373313980.09423215024270.05567312410390.372105607958-0.009437767241040.001733293659920.343028315822-0.04829909619140.350456960778-5.148178816656.599529986122.9634919393
102.26941200472-3.37732770062.035460213138.67707471937-7.937796613888.23770451841-0.101893181548-0.1312752167570.2934243536130.0736060564883-0.23915136102-0.376691114751-0.1324902108760.3137974778250.4396473737980.3417166394010.0149200470399-0.05016089323990.351359451448-0.004524458354810.301794569061-12.070065268169.939490760729.6223478596
116.48546195218-0.340361013573-1.288634862981.133728918930.6132807213922.5256839769-0.1226147838710.322796996695-0.4342804788580.03149838781480.110657157453-0.1515470830580.1678324254320.2027856618010.006011797537530.35842893080.0331673460407-0.02016534390310.318122438623-0.05926904654310.357538601355-2.1846040872553.504596715121.2156604094
121.336082783160.338388155198-0.4359681482572.493026634331.216555643382.955241678340.01155864150360.0111695926194-0.0214012569066-0.182828175522-0.1465957378250.39052436168-0.149087357436-0.5095205510970.182650590290.2849539321450.0211807845452-0.04201313644230.360845932454-0.01483077767950.285895964964-21.987776831565.257933291226.7369567656
134.93232869286-2.2532972766-1.271946344452.5457363231.210075858052.65660150268-0.409754231475-0.113111764676-0.2163621385180.189284976470.0001629843235880.655314597639-0.0084309165583-0.1380722773560.4460771299670.4290578948750.1009119808580.04129447641520.3284468611370.02557984317510.53869351268620.238829678532.04990475949.86443463678
149.51901952649-3.85890368663-5.809972503253.130763894642.053736542253.842456866620.03728842406850.522595697139-0.0484120824559-0.02464060183670.02535868959560.228349623906-0.119949353078-0.4764602968070.08863944423450.292928806012-0.00715617836443-0.04110568393030.3349049542220.02144116214940.30407202561532.495530451423.43416394726.11466754466
153.16639691268-0.315963392464-0.6556042549323.280453323470.3136721437780.950756204951-0.06222695575510.0762109090534-0.1090377636450.19626989804-0.06095789402080.592817031713-0.243998373781-0.4179275362160.1078279164250.4009193965170.1330988047060.03941283788320.418895679975-0.01948734477670.49112303467915.387833161935.277694012110.5745984451
165.67987483844-0.864876941622-0.4217165675851.980634927721.534913129384.46189927157-0.09437292804720.1726106901320.367868327849-0.01597679243550.1102224406150.181196847703-0.1833832675110.162841247424-0.07289926661960.277741501232-0.0176420061504-0.01175008063960.2620833983850.07839662242490.25687240246237.889530858931.27845429299.49197399399
177.12119690385.476772999030.1535176145869.60804061611-1.33645707913.300656665430.242706420684-0.4777736438980.09035204189790.0370281555287-0.597901975849-0.689574527397-0.1230410096960.4220085415970.3275539329120.372498210159-0.01425853280270.04161299918620.3815417810340.0914906108670.42634944546-23.432178118314.843468484225.8806322741
181.240691308760.61276829603-0.04390793179664.78576282668-0.9729454726152.85048601380.1923846053680.05785693868590.0268741548424-0.150748232042-0.1479112110780.197054807880.230908283739-0.230056940939-0.06975874167040.332972469606-0.0240188448020.01654136821820.347709414645-0.02285640034280.314310303589-31.2910009445-5.6803742882921.114124722
190.5246594748440.578527306024-0.9715047014493.51215062512-1.485135224832.844751635870.05654542805650.08791773048440.0405921678491-0.141085594111-0.0356600658442-0.00712990145133-0.153818679992-0.09190715692060.009205422539760.332660404523-0.0107639539238-0.008446082124710.342289496151-0.0188025778250.287327431742-29.526619132-2.8117005231226.9115954182
208.16110939068-3.42077941785-2.429035274098.869603586-2.670968893533.354074562430.4889771631970.00978371814710.835963027677-0.690748383108-0.715764303199-0.444243241502-0.3387855371150.2307292381740.1217756206550.3467868226390.007681193697820.07802208612270.3417622345230.08124247173370.428429904595-27.611458623118.092429715420.1598702046
212.528840938640.931099637865-0.7805625032950.869363693793-0.5213695163352.6806923455-0.2360765578890.0625223163095-0.401055795804-0.1051934943040.0543094753711-0.1832644259430.501961366343-0.0831938547630.1890922795650.3936950520020.0009673554979730.01972663329550.293230621769-0.0124619813640.323590973022-26.1440486433-13.39510301628.1177468952
221.15281466133-0.0371009134399-0.5540908305113.81910537564-1.881143699272.12627875903-0.109863925996-0.0399509085986-0.539638849677-0.0812071739201-0.169963200066-0.2050682241080.1288027819450.02960780609850.3458191746090.457552368259-0.0693271163093-0.03223594390060.3128659866540.009779228726580.524568279482-17.00853270438.841326636110.0369762415
232.09402343932-0.4032259207290.7399687180053.99263347999-2.166110677812.722242870980.0939587918728-0.065613651521-0.360654276866-0.367677442096-0.202225279504-0.2403137111290.3341160358190.1138514812920.1277481209640.406511611764-0.00595795496683-0.001301492405970.312161134498-0.02254961955730.379525161853-16.682074909739.59386593259.37656834582
241.3800759043-0.51683565356-1.606829848762.85248412456-2.853363303726.442810779090.168340620763-0.0452469395596-0.257198030479-0.353982054099-0.2377781009340.275934581734-0.247219626634-0.3996906443990.008561649985540.3189527962250.00400326342827-0.08824167718180.33764351039-0.04760795885350.363041746455-24.846746481954.49589122088.88558552084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 32 )
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 51 )
5X-RAY DIFFRACTION5chain 'C' and (resid 7 through 17 )
6X-RAY DIFFRACTION6chain 'C' and (resid 18 through 22 )
7X-RAY DIFFRACTION7chain 'C' and (resid 23 through 32 )
8X-RAY DIFFRACTION8chain 'D' and (resid 43 through 51 )
9X-RAY DIFFRACTION9chain 'E' and (resid 7 through 17 )
10X-RAY DIFFRACTION10chain 'E' and (resid 18 through 22 )
11X-RAY DIFFRACTION11chain 'E' and (resid 23 through 32 )
12X-RAY DIFFRACTION12chain 'F' and (resid 43 through 51 )
13X-RAY DIFFRACTION13chain 'G' and (resid 7 through 17 )
14X-RAY DIFFRACTION14chain 'G' and (resid 18 through 22 )
15X-RAY DIFFRACTION15chain 'G' and (resid 23 through 32 )
16X-RAY DIFFRACTION16chain 'H' and (resid 43 through 51 )
17X-RAY DIFFRACTION17chain 'I' and (resid 7 through 12 )
18X-RAY DIFFRACTION18chain 'I' and (resid 13 through 17 )
19X-RAY DIFFRACTION19chain 'I' and (resid 18 through 27 )
20X-RAY DIFFRACTION20chain 'I' and (resid 28 through 32 )
21X-RAY DIFFRACTION21chain 'J' and (resid 43 through 51 )
22X-RAY DIFFRACTION22chain 'K' and (resid 7 through 17 )
23X-RAY DIFFRACTION23chain 'K' and (resid 18 through 32 )
24X-RAY DIFFRACTION24chain 'L' and (resid 43 through 51 )

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