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- PDB-6ymm: Crystal structure of the SAM-SAH riboswitch with SAM from space g... -

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Basic information

Entry
Database: PDB / ID: 6ymm
TitleCrystal structure of the SAM-SAH riboswitch with SAM from space group P312
Components
  • Chains: A
  • Chains: B,D
KeywordsRNA / Pseudoknot / SAM / Riboswitch
Function / homologyS-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
Biological speciesRoseobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Chains: B,D
C: Chains: A
D: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7908
Polymers22,5714
Non-polymers1,2184
Water19811
1
A: Chains: A
B: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1065
Polymers11,2862
Non-polymers8203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chains: A
D: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6843
Polymers11,2862
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.170, 88.170, 76.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: -y,-x,-z
#5: -x+y,y,-z
#6: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

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Components

#1: RNA chain Chains: A


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


Mass: 2895.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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 / Wavelength: 0.9198 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.2→76.08 Å / Num. obs: 32912 / % possible obs: 99.6 % / Redundancy: 14.2 % / Biso Wilson estimate: 61.11 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.022 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 801 / CC1/2: 0.696 / Rpim(I) all: 0.52 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→38.18 Å / SU ML: 0.4099 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.4545
RfactorNum. reflection% reflection
Rfree0.2211 1688 5.13 %
Rwork0.1923 --
obs0.1939 32912 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1484 67 11 1562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761728
X-RAY DIFFRACTIONf_angle_d1.63952681
X-RAY DIFFRACTIONf_chiral_restr0.1223356
X-RAY DIFFRACTIONf_plane_restr0.010173
X-RAY DIFFRACTIONf_dihedral_angle_d17.0192857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.38241150.43522402X-RAY DIFFRACTION91.33
2.26-2.340.44051060.40712568X-RAY DIFFRACTION95.5
2.34-2.420.45741760.37642518X-RAY DIFFRACTION96.32
2.42-2.520.35841400.36772571X-RAY DIFFRACTION96.75
2.52-2.630.39571270.34692633X-RAY DIFFRACTION98.05
2.63-2.770.41441350.32082620X-RAY DIFFRACTION98.96
2.77-2.950.3451210.30472669X-RAY DIFFRACTION99.32
2.95-3.170.25561420.22982647X-RAY DIFFRACTION99.79
3.17-3.490.21491640.1842632X-RAY DIFFRACTION99.96
3.49-40.22251570.16942666X-RAY DIFFRACTION99.93
4-5.030.17361350.14042647X-RAY DIFFRACTION100
5.03-38.180.14131700.1292651X-RAY DIFFRACTION99.79
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)
15.396046680114.02334299953.370716005856.32173626566-0.8905382127195.87801855942-0.6606009034730.637729361803-1.1266042779-0.1067603455270.312547471305-0.5477683526140.1170536853360.5013468570480.2985170445110.653681057136-0.01506979053330.1042889673560.693602185426-0.05052136391360.59009111013523.1870454325-11.102514073726.1683361559
25.139339560570.790347833401-0.9418037360531.27903084366-0.1852095093740.8151181907530.04071350392330.1088700448040.0552266128765-0.1131003638750.05654876696140.00658991256924-0.1191998461920.0241220342388-0.1310167426980.645942354563-0.0332189115193-0.01141731163920.633069229274-0.05040771677080.5006350619293.51946956502-14.394430051224.8616472359
38.485904942383.996502901884.788708409736.037346745821.598982297784.05516333377-0.350775723321-0.39584883528-0.0516253889525-0.1265807958960.268155449982-0.5500697435360.1188792384890.2788022032210.006384924891720.6675118986370.003067974120120.1440610826290.798991654934-0.107719032140.66181068443623.7756047013-5.6280867558220.5292256215
42.68849009678-1.91730272839-0.7275958725541.37205447217-0.07348856178382.00139133570.2036026098240.435683481839-0.303113655416-0.019411686631-0.2861275345190.0628771983306-0.00578622581382-0.1478748828870.1294167687280.599436846414-0.0275382468446-0.06227614989680.697909994508-0.03569847541840.555744253362-2.92328997352-22.64246279128.2094719207
57.835786798894.20653864991-6.023655083094.82429692616-2.414602897024.87667625724-0.7078554252310.323137945836-0.718143224601-0.639123822748-0.1933798942510.4608706517920.510494427624-0.2435053660850.836828347540.689734937278-0.11327468503-0.0590912916621.03417247460.01815622708920.97931075979347.8961670681-3.0005098088511.5796008234
64.545631509092.70545049426-3.107452252747.61615814381-0.6753314437912.05489733452-0.7858822102340.721798645067-0.257211599312-0.6708671299640.4719083410090.9774389262640.64563880187-0.6283685202610.3900304480470.795514544322-0.165756555309-0.08927366354731.024215330730.03954392536330.80327903350949.1685823636-2.8481388126810.8928273264
72.251585496923.411981312980.7590044282459.28663784995-1.602811202054.14278543316-0.3724253750420.8775334767010.273375577271-0.5292020970020.3662885693490.97254800985-0.486967022971-0.6859577004570.03486594480780.6602725404730.00401971354982-0.09322166936950.8156518461660.04584078952230.590381475658.150159046811.756862308110.8390224083
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 32 )
7X-RAY DIFFRACTION7chain 'D' and (resid 43 through 51 )

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