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- PDB-6fz6: Crystal Structure of a radical SAM methyltransferase from Sphaero... -

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Basic information

Entry
Database: PDB / ID: 6fz6
TitleCrystal Structure of a radical SAM methyltransferase from Sphaerobacter thermophilus
ComponentsProbable dual-specificity RNA methyltransferase RlmN
KeywordsTRANSFERASE / Radical SAM / rRNA / methyltransferase / antibiotic resistance
Function / homology
Function and homology information


23S rRNA (adenine2503-C2)-methyltransferase / tRNA (adenine(37)-C2)-methyltransferase activity / rRNA (adenine(2503)-C2-)-methyltransferase activity / rRNA base methylation / 4 iron, 4 sulfur cluster binding / tRNA binding / rRNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal RNA large subunit methyltransferase RlmN/Cfr / Dual-specificity RNA methyltransferase RlmN / Methyltransferase (Class A) / Radical SAM superfamily / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / Probable dual-specificity RNA methyltransferase RlmN
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
AuthorsHinchliffe, P. / Shaw, J.M. / Spencer, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J017906/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M012107/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal Structure of a radical SAM methyltransferase from Sphaerobacter thermophilus
Authors: Shaw, J.M. / Hinchliffe, P. / Spencer, J.
History
DepositionMar 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable dual-specificity RNA methyltransferase RlmN
B: Probable dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1189
Polymers81,3942
Non-polymers1,7247
Water11,458636
1
A: Probable dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6055
Polymers40,6971
Non-polymers9084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5134
Polymers40,6971
Non-polymers8163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.840, 53.140, 113.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21B-808-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable dual-specificity RNA methyltransferase RlmN / 23S rRNA (adenine(2503)-C(2))-methyltransferase / 23S rRNA m2A2503 methyltransferase / Ribosomal ...23S rRNA (adenine(2503)-C(2))-methyltransferase / 23S rRNA m2A2503 methyltransferase / Ribosomal RNA large subunit methyltransferase N / tRNA (adenine(37)-C(2))-methyltransferase / tRNA m2A37 methyltransferase


Mass: 40696.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (strain DSM 20745 / S 6022) (bacteria)
Strain: DSM 20745 / S 6022 / Gene: rlmN, Sthe_1821 / Production host: Escherichia coli (E. coli)
References: UniProt: D1C4T7, 23S rRNA (adenine2503-C2)-methyltransferase

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Non-polymers , 5 types, 643 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Fe4S4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide, 0.1 M HEPES/MOPS pH 7.5, 20 % Glycerol, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.42→57.01 Å / Num. obs: 150914 / % possible obs: 99.99 % / Redundancy: 13.07 % / CC1/2: 0.9971 / Rmerge(I) obs: 0.1318 / Net I/σ(I): 9.65
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 2.6908 / Mean I/σ(I) obs: 0.95 / CC1/2: 0.4936 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.42→49.287 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.1871 7363 4.88 %
Rwork0.1661 --
obs0.1671 150914 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.42→49.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5312 0 76 636 6024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015544
X-RAY DIFFRACTIONf_angle_d1.1097548
X-RAY DIFFRACTIONf_dihedral_angle_d15.052099
X-RAY DIFFRACTIONf_chiral_restr0.11873
X-RAY DIFFRACTIONf_plane_restr0.007982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.43610.34112550.35274777X-RAY DIFFRACTION100
1.4361-1.4530.34682400.33324680X-RAY DIFFRACTION100
1.453-1.47080.35112630.32074722X-RAY DIFFRACTION100
1.4708-1.48940.3532360.29724721X-RAY DIFFRACTION100
1.4894-1.5090.29522360.28734754X-RAY DIFFRACTION100
1.509-1.52960.25772590.25914734X-RAY DIFFRACTION100
1.5296-1.55150.27132430.24054735X-RAY DIFFRACTION100
1.5515-1.57470.23992450.22384721X-RAY DIFFRACTION100
1.5747-1.59930.22742480.21044722X-RAY DIFFRACTION100
1.5993-1.62550.23272270.19794779X-RAY DIFFRACTION100
1.6255-1.65350.21232280.1934776X-RAY DIFFRACTION100
1.6535-1.68360.21822290.1874730X-RAY DIFFRACTION100
1.6836-1.7160.20382670.18354768X-RAY DIFFRACTION100
1.716-1.7510.20542360.16644725X-RAY DIFFRACTION100
1.751-1.78910.18462350.16284768X-RAY DIFFRACTION100
1.7891-1.83070.18272720.15844761X-RAY DIFFRACTION100
1.8307-1.87650.18622220.15614755X-RAY DIFFRACTION100
1.8765-1.92720.1682250.15694789X-RAY DIFFRACTION100
1.9272-1.98390.17132370.15224770X-RAY DIFFRACTION100
1.9839-2.0480.18022390.15364808X-RAY DIFFRACTION100
2.048-2.12120.17512540.15724766X-RAY DIFFRACTION100
2.1212-2.20610.18422440.15414780X-RAY DIFFRACTION100
2.2061-2.30650.17862570.15784793X-RAY DIFFRACTION100
2.3065-2.42810.16382730.15834786X-RAY DIFFRACTION100
2.4281-2.58020.19922330.15714812X-RAY DIFFRACTION100
2.5802-2.77940.1712560.16064826X-RAY DIFFRACTION100
2.7794-3.05910.19122480.16184840X-RAY DIFFRACTION100
3.0591-3.50160.18222520.15844879X-RAY DIFFRACTION100
3.5016-4.41130.15772390.14154947X-RAY DIFFRACTION100
4.4113-49.31670.16972650.15525127X-RAY DIFFRACTION100
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)
10.811-0.34030.60241.47210.13462.0859-0.0043-0.17680.09560.11110.0305-0.0393-0.03630.021-0.00920.17990.00490.0040.2142-0.03480.1695-9.591115.8885-35.4074
20.87660.0592-0.16410.41240.03710.56040.00450.0770.0908-0.0335-0.00870.0029-0.0472-0.02990.00640.14950.0012-0.00180.15080.00190.1664-13.233710.9897-54.7632
30.7277-0.4262-0.42211.97841.54862.05790.0061-0.1046-0.04330.21420.06080.01130.10110.0360.03310.1899-0.0040.00250.19270.00340.187-15.939-3.8992-49.0839
43.1199-0.24031.3261.1778-0.77381.12770.00480.4634-0.2839-0.05840.0799-0.07470.08350.2029-0.01940.19570.0027-0.0150.2701-0.0780.2033-9.9832-11.8053-70.175
50.8578-0.33310.61981.0592-0.01081.93380.03120.1461-0.11770.00690.0149-0.02730.0786-0.04820.02080.1645-0.0336-0.00620.1885-0.020.1688-20.8691-10.2071-67.2042
61.39891.09950.00731.96-0.13660.85380.12720.04060.16920.0846-0.15190.2081-0.1636-0.20450.02590.1716-0.0199-0.01540.2430.00880.1789-29.0856-3.6989-70.8833
76.81763.21462.07353.76792.83885.4677-0.16540.33770.356-0.44040.1757-0.1409-0.51490.4430.00150.3655-0.06470.02680.3780.04550.3049-11.653111.8432-68.6861
81.0559-0.06850.29340.88920.03282.45840.0106-0.30890.24950.11310.0596-0.0314-0.25150.08850.0170.22220.00280.02220.246-0.08210.2216-12.391242.017817.8832
90.7883-0.0969-0.02470.74420.29820.5412-0.0087-0.04950.0190.00590.03420.0682-0.0019-0.09240.00550.1473-0.00640.00980.14110.00810.1475-14.476427.2331-0.2534
101.3588-0.53760.38220.9758-0.07642.0878-0.00350.1618-0.20170.0167-0.04390.07220.0615-0.15530.01170.1184-0.04830.00420.1308-0.01420.1509-18.579813.127-11.1541
111.05241.0389-0.12032.5734-0.35470.96970.02650.22130.13250.1134-0.12710.3748-0.1591-0.41610.0260.1796-0.0233-0.01110.302-0.03330.2515-27.81818.0536-14.7422
126.58022.58352.13984.5233.96654.0956-0.1290.48760.5989-0.43920.1696-0.1518-0.6570.3828-0.05730.4206-0.01790.00440.45090.06550.3977-13.608436.2069-12.3444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 235 )
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 333 )
7X-RAY DIFFRACTION7chain 'A' and (resid 335 through 340 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 70 )
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 235 )
10X-RAY DIFFRACTION10chain 'B' and (resid 236 through 302 )
11X-RAY DIFFRACTION11chain 'B' and (resid 303 through 333 )
12X-RAY DIFFRACTION12chain 'B' and (resid 335 through 340 )

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