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

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Basic information

Entry
Database: PDB / ID: 6ylb
TitleCrystal structure of the SAM-SAH riboswitch with SAM
Components
  • Chains: A,C,F,I,M,O
  • Chains: B,D,G,J,N,P
KeywordsRNA / Pseudoknot / SAM / Riboswitch
Function / homologyS-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
Biological speciesRoseobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chains: A,C,F,I,M,O
B: Chains: B,D,G,J,N,P
C: Chains: A,C,F,I,M,O
D: Chains: B,D,G,J,N,P
F: Chains: A,C,F,I,M,O
G: Chains: B,D,G,J,N,P
I: Chains: A,C,F,I,M,O
J: Chains: B,D,G,J,N,P
M: Chains: A,C,F,I,M,O
N: Chains: B,D,G,J,N,P
O: Chains: A,C,F,I,M,O
P: Chains: B,D,G,J,N,P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,30021
Polymers67,71412
Non-polymers3,5869
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14200 Å2
ΔGint-9 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.113, 147.937, 74.839
Angle α, β, γ (deg.)90.000, 91.707, 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

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Components

#1: RNA chain
Chains: A,C,F,I,M,O


Mass: 8389.874 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#2: RNA chain
Chains: B,D,G,J,N,P


Mass: 2895.791 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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: 0.9119 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: 0.9119 Å / Relative weight: 1
ReflectionResolution: 2.12→75.04 Å / Num. obs: 98596 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 57.35 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.056 / Net I/σ(I): 7.4
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.15 / Num. unique obs: 2658 / CC1/2: 0.36 / Rpim(I) all: 0.76 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YL5
Resolution: 2.12→37.46 Å / SU ML: 0.4024 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2627 4850 4.92 %
Rwork0.2248 93746 -
obs0.2266 98596 93.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.79 Å2
Refinement stepCycle: LAST / Resolution: 2.12→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4452 193 95 4740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725179
X-RAY DIFFRACTIONf_angle_d1.22328038
X-RAY DIFFRACTIONf_chiral_restr0.0531068
X-RAY DIFFRACTIONf_plane_restr0.009219
X-RAY DIFFRACTIONf_dihedral_angle_d15.12432566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.140.4601890.39391983X-RAY DIFFRACTION58.53
2.14-2.170.3777910.36892114X-RAY DIFFRACTION62.25
2.17-2.20.34851250.36832391X-RAY DIFFRACTION71.15
2.2-2.220.38171670.35732847X-RAY DIFFRACTION86.48
2.22-2.250.37191810.36193250X-RAY DIFFRACTION96.4
2.25-2.280.32511620.35343289X-RAY DIFFRACTION97.62
2.28-2.320.39551930.3483233X-RAY DIFFRACTION97.58
2.32-2.350.33531730.33963267X-RAY DIFFRACTION97.09
2.35-2.390.38572190.34373223X-RAY DIFFRACTION97.15
2.39-2.430.32292670.34023075X-RAY DIFFRACTION96.37
2.43-2.470.34932160.32823237X-RAY DIFFRACTION96.7
2.47-2.510.39631470.33113348X-RAY DIFFRACTION97.57
2.51-2.560.33341630.31173234X-RAY DIFFRACTION97.5
2.56-2.610.3612090.32943206X-RAY DIFFRACTION97.24
2.61-2.670.33992490.32253219X-RAY DIFFRACTION97.03
2.67-2.730.35931420.32133248X-RAY DIFFRACTION96.8
2.73-2.80.39221800.3053245X-RAY DIFFRACTION96.64
2.8-2.880.41661240.29513265X-RAY DIFFRACTION95.9
2.88-2.960.2576940.27833281X-RAY DIFFRACTION95.23
2.96-3.060.27541040.25943237X-RAY DIFFRACTION94.11
3.06-3.170.2921410.25793088X-RAY DIFFRACTION92.73
3.17-3.290.29351460.23453276X-RAY DIFFRACTION96.86
3.29-3.440.23921630.21273288X-RAY DIFFRACTION97.27
3.44-3.620.21511200.20613248X-RAY DIFFRACTION95.76
3.62-3.850.23481710.18953298X-RAY DIFFRACTION98.11
3.85-4.150.24981150.19353383X-RAY DIFFRACTION98.7
4.15-4.560.24471680.18553277X-RAY DIFFRACTION97.51
4.57-5.220.28381470.17793188X-RAY DIFFRACTION95.01
5.22-6.580.19641420.16963268X-RAY DIFFRACTION95.79
6.58-37.460.16572420.14333240X-RAY DIFFRACTION98.33
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)
14.198225133950.4976759996890.08026862291491.044665185050.00480080860612-0.320535276556-0.07724451221570.04239388188310.499453671128-0.374215149410.08407078244730.283059486604-0.0271122038162-0.1010752649330.04709478149710.539554486358-0.0462251286919-0.03992537196190.5097035568930.004740212765540.44169180924534.264922069812.599120485625.1824110713
20.3711703720850.36424535325-0.2641247389592.47731802793-0.6028631489411.69342274534-0.08382810268320.21586516287-0.0090231940171-0.4387689550960.2607430937930.2569639587980.0450691048721-0.183305762907-0.08146509390150.516791150814-0.0125642735647-0.0781913676820.6764267217740.04545880124520.55017269428525.717640593311.827352578221.0552424369
30.754448116993-0.197653614090.9239314682030.330240055046-0.3229078264620.3867499531170.0879542120023-0.2281402721170.07396008574990.503248510325-0.008695538191630.290834133276-0.2951861613240.0153003154163-0.1449010194090.519618197205-0.0477698527190.07857423776670.5736783502790.007700742312280.60550907604845.475210433222.992449493627.5443765552
42.94321145725-0.2830469172892.180974170390.987635676638-0.7412619875791.66075683097-0.5756996521920.3169316629480.880264922469-0.315137450248-0.0276204460214-1.1466662045-0.2351331652220.289367659990.6644876396910.542074212292-0.172472307964-0.09069921156731.02217795807-0.06801586232760.981896537115-4.570922071063.9915070299311.6439210722
52.626792612381.01502036116-0.1379207975355.44461098034.17015746363.65097415774-0.10786697719-0.0348455495477-0.48204886853-0.5670159874240.1895273718590.119351210774-0.3098972722870.938772078016-0.111694756180.551426472562-0.1072089499340.07021658807660.663742320778-0.0267182429180.358410774971-18.2225710902-2.156284771117.45269327746
61.36577320121-0.517157922404-0.9722174278641.377034088740.06392016758272.51051873295-0.7477045061220.5465500125170.1359691946220.1751336586670.412316570029-1.01143847666-0.3592082469590.07220062108430.4172060271130.673835450063-0.309279637893-0.1580233404260.8836636310920.005155694056390.9481436002870.1960513011586.7661884916412.7119763762
71.885634346541.017410630940.9890736237344.0732183815-0.3725359475184.642367909460.128722732808-0.7744639569410.0698426774186-0.6094043234660.166152976322-0.6895051940830.813840162126-0.134716207123-0.1484527474460.6586859291620.02022111164870.03966656464110.709034882512-0.1616229857880.618218583107-14.3698871627-10.697933300111.1503954807
81.083235782050.6632072883670.86235491060.981125092241-0.6743782134811.06869190189-0.2064592370670.39364364176-0.3166982941120.1757743015520.1259241751340.1236300508290.01321588370860.04551541506440.004438308565990.5016565553770.04077931136930.03974664439960.569215896839-0.07692652436950.363985596574-4.9986026737756.772341898123.0523928497
92.27399235022-2.33386042771.84838705662.88262225553-2.651396629744.69080234576-0.265717129314-0.3113576486910.235790346366-0.294835499702-0.203226386957-0.1575933505620.293195857249-0.1728408415410.6162511894540.4201586322560.02725687160210.0061310259660.6056383450160.1070233263870.400644959301-11.766980324470.181312695329.8217347782
102.406001296710.9584202131230.03672019597430.4711629961320.06777484246220.8971816534330.05476144963690.464495796852-0.299915318896-0.4119942411310.169047185810.05004409287660.2062132183350.00602980744938-0.1939716111180.5877698649590.0617290142811-0.01130299598940.480396761575-0.03791956706630.404860630363-1.9672186033953.701088792921.2925512913
111.21233187770.118188252606-0.1698849765331.053047230371.291371373911.151394990630.216525261946-0.41937771074-0.09777013897080.3224988396590.0511971995772-0.5519167647380.240542099975-0.416179548610.06152365894850.526894887090.0467203882178-0.02664519464650.5692831592580.03070518241690.493967544876-21.709905296565.440449032826.951169484
120.9952575246240.1896429368130.522219547771.783679440421.327087780092.82817092084-0.3349867738080.3372812026190.1621853859170.192390829465-0.5102443833540.704724230926-0.0410320564071-0.3111571042730.776341694960.7539685543760.1668587834660.07365318050730.6238863862740.09016043642721.0912375896420.643416297732.286956460110.0182232249
134.81958566523-0.69497745262-3.578873061232.0420227819-0.2980728221393.194122124740.03025567621670.956034649941.159122838390.08050067763340.2008935126480.424052069766-0.145727440236-0.5262577164140.1455271934950.6536901827440.102838851219-0.04763859616350.644720778180.2233473275170.64854694721332.697638012223.57899644286.19185091486
140.2791668400870.52219885857-0.1871410676041.14358673490.4138851478140.927949938331-0.117489237612-0.09070531139580.9070853391790.14760442335-0.3773290266090.617608516060.0906089994-0.2828249666350.5857391812120.6414167106890.1909004616050.04539922073910.759980846065-0.1426031549271.3670442089715.813145329635.38720786410.7016017454
152.669819435151.833594914350.9651208995261.344755350060.5267614281384.44261518917-0.292329367915-0.07761291756240.3575349665860.2923042740470.3115033151890.814792993439-0.248454670070.806959174233-0.07042790731110.583106193082-0.04611719365320.03738256293130.5294558087230.09930837537580.66171375616438.213549928531.34951300759.69439878344
160.8011146793190.0964234070437-0.05416143543712.961178050310.7257310179110.585650071510.1966136345870.08894742122130.0354895531421-0.363744223216-0.252274766064-0.21466818076-0.114331979532-0.007512841294930.1476341810230.5176207888290.0005051151781560.03916486861470.5253341322070.01417660314710.358066827981-29.64223463821.6689227344625.7078279808
171.8178812229-1.20295845172-0.4795514178281.72923178290.4981933389671.251600732290.3478850819380.4950699414480.244137412177-0.300129293923-0.4676950659940.208173487785-0.2075162970660.2374765526960.03480770821890.616012680675-0.139610629880.07779562391170.5111766033950.007376376966490.480613798089-25.87861405589.5264708598621.8887320141
181.530555125840.171992565954-0.3958989029281.22209749139-0.5756205528711.09672862475-0.0321308323454-0.5445136959590.533225169342-0.21452623160.08513797081950.3284566734850.2940797672480.3910736167950.1353326264860.578348937954-0.0440719135191-0.02608101959550.520374833403-0.05566585346510.372027902254-26.3139885029-13.363264639728.1165111683
191.892546295920.565176684152-0.8204079588330.414070430485-0.4748096435272.57299270475-0.242873313020.0872741729303-1.13800874271-0.0344741035709-0.3963594306130.08126415692760.2765344498110.08261085720520.9063133625460.770795513851-0.0834312321623-0.002511626073770.4951727060740.04379481511011.07686223865-17.303607231138.939564976310.1636318157
201.90631615105-0.555142577067-1.040224982972.41830918599-1.375623989061.49664165613-0.18090399307-0.415205681409-1.02927278565-0.204016044172-0.05607716373090.6536195663550.542403122241-0.1128298891180.2787827557130.828607572212-0.0565305600909-0.05612706100420.4437711124250.06890297878060.971387750898-16.841126336339.72405426699.40188368658
212.85954347644-1.17283208896-1.187127028364.69239379576-1.37944855675.934790270530.628680949964-0.341900704048-1.16669523390.0128214880203-1.008257741150.917265247858-0.659675217282-0.4738909329450.2235616109790.525345181045-0.00225116302177-0.214913741230.581639727305-0.02961044753970.722689010848-24.892826068254.6210014759.19635835963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 32 )
3X-RAY DIFFRACTION3chain 'B' and (resid 43 through 51 )
4X-RAY DIFFRACTION4chain 'C' and (resid 7 through 17 )
5X-RAY DIFFRACTION5chain 'C' and (resid 18 through 22 )
6X-RAY DIFFRACTION6chain 'C' and (resid 23 through 32 )
7X-RAY DIFFRACTION7chain 'D' and (resid 43 through 51 )
8X-RAY DIFFRACTION8chain 'F' and (resid 7 through 17 )
9X-RAY DIFFRACTION9chain 'F' and (resid 18 through 22 )
10X-RAY DIFFRACTION10chain 'F' and (resid 23 through 32 )
11X-RAY DIFFRACTION11chain 'G' and (resid 43 through 51 )
12X-RAY DIFFRACTION12chain 'I' and (resid 7 through 17 )
13X-RAY DIFFRACTION13chain 'I' and (resid 18 through 22 )
14X-RAY DIFFRACTION14chain 'I' and (resid 23 through 32 )
15X-RAY DIFFRACTION15chain 'J' and (resid 43 through 51 )
16X-RAY DIFFRACTION16chain 'M' and (resid 7 through 22 )
17X-RAY DIFFRACTION17chain 'M' and (resid 23 through 32 )
18X-RAY DIFFRACTION18chain 'N' and (resid 43 through 51 )
19X-RAY DIFFRACTION19chain 'O' and (resid 7 through 17 )
20X-RAY DIFFRACTION20chain 'O' and (resid 18 through 32 )
21X-RAY DIFFRACTION21chain 'P' and (resid 43 through 51 )

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