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- PDB-3m6w: Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 3m6w
TitleMulti-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P21212 in complex with S-Adenosyl-L-Methionine
ComponentsrRNA methylase
KeywordsTRANSFERASE / rRNA methyltransferase / 5-methylcytidine / RsmF / AdoMet / multi-specific / methyltransferase
Function / homology
Function and homology information


16S rRNA (cytosine1407-C5)-methyltransferase / RNA methyltransferase activity / RNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing / RNA binding / cytoplasm
Similarity search - Function
: / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #60 / Ribosomal RNA small subunit methyltransferase F, first C-terminal domain / RsmF rRNA methyltransferase first C-terminal domain / Sun protein; domain 3 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / : / SAM-dependent methyltransferase RsmB/NOP2-type ...: / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #60 / Ribosomal RNA small subunit methyltransferase F, first C-terminal domain / RsmF rRNA methyltransferase first C-terminal domain / Sun protein; domain 3 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / : / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Vaccinia Virus protein VP39 / Roll / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Ribosomal RNA small subunit methyltransferase F
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsDemirci, H. / Larsen, H.G.L. / Hansen, T. / Rasmussen, A. / Cadambi, A. / Gregory, S.T. / Kirpekar, F. / Jogl, G.
CitationJournal: Rna / Year: 2010
Title: Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.
Authors: Demirci, H. / Larsen, L.H. / Hansen, T. / Rasmussen, A. / Cadambi, A. / Gregory, S.T. / Kirpekar, F. / Jogl, G.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3563
Polymers50,9231
Non-polymers4342
Water15,421856
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: rRNA methylase
hetero molecules

A: rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7136
Polymers101,8452
Non-polymers8684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1810 Å2
ΔGint-26 kcal/mol
Surface area36150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.661, 109.047, 50.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-827-

HOH

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Components

#1: Protein rRNA methylase


Mass: 50922.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RsmF minus / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1387 / Plasmid: pLJ102 / Production host: Escherichia coli (E. coli) / Strain (production host): CP79
References: UniProt: Q5SII2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 10% w/v PEG1000, 200 mM NaCl and 100 mM TRIS-HCl (pH8.5), microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2008
Details: Slits: Variable vertical and fixed horizontal slits. Mirror: Mirror system consisting of two vertically stacked, fused silica, spherical mirrors, to provide vertical focusing and harmonic ...Details: Slits: Variable vertical and fixed horizontal slits. Mirror: Mirror system consisting of two vertically stacked, fused silica, spherical mirrors, to provide vertical focusing and harmonic rejection. One of the mirrors is rhodium coated and the other is uncoated. Located ~19.7 m from source.
RadiationMonochromator: KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source ...Monochromator: KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source and ~6 m from sample position.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionRedundancy: 5.2 % / Av σ(I) over netI: 24.3 / Number: 633624 / Rmerge(I) obs: 0.058 / Χ2: 1.02 / D res high: 1.29 Å / D res low: 30 Å / Num. obs: 121660 / % possible obs: 95.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.783097.310.0381.0415.6
2.212.7810010.0561.0016
1.932.2110010.0731.095.9
1.751.9310010.0951.1035.9
1.631.7510010.1231.0325.8
1.531.6310010.161.0255.8
1.451.5310010.2230.9955.6
1.391.4599.810.2980.9454.9
1.341.3992.510.330.8693.2
1.291.3466.310.3560.8162.1
ReflectionResolution: 1.29→30 Å / Num. obs: 121660 / % possible obs: 95.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.058 / Χ2: 1.019 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.29-1.342.10.35683550.816166.3
1.34-1.393.20.33116220.869192.5
1.39-1.454.90.298125900.945199.8
1.45-1.535.60.223125850.9951100
1.53-1.635.80.16126131.0251100
1.63-1.755.80.123126841.0321100
1.75-1.935.90.095126781.1031100
1.93-2.215.90.073127741.091100
2.21-2.7860.056128411.0011100
2.78-305.60.038129181.041197.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M6U

3m6u


Resolution: 1.3→29.597 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.893 / SU ML: 0.17 / σ(F): 1.33 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 6036 5.05 %
Rwork0.177 --
obs0.178 119490 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.211 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 84.79 Å2 / Biso mean: 19.302 Å2 / Biso min: 7.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.011 Å20 Å2-0 Å2
2--0.352 Å2-0 Å2
3----0.363 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 28 856 4441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053744
X-RAY DIFFRACTIONf_angle_d1.1355104
X-RAY DIFFRACTIONf_chiral_restr0.068535
X-RAY DIFFRACTIONf_plane_restr0.007674
X-RAY DIFFRACTIONf_dihedral_angle_d17.7861416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.3150.2341280.2332512264065
1.315-1.330.2261720.2282960313277
1.33-1.3470.2741660.2263286345285
1.347-1.3630.2182000.2163565376592
1.363-1.3810.2221850.2083746393196
1.381-1.40.2182050.1983823402899
1.4-1.420.2161840.18738754059100
1.42-1.4420.2261620.18839154077100
1.442-1.4640.1922070.17438704077100
1.464-1.4880.1962020.16838744076100
1.488-1.5140.1872360.16938224058100
1.514-1.5410.1532030.1639194122100
1.541-1.5710.1752220.15638074029100
1.571-1.6030.1911850.15939364121100
1.603-1.6380.1771900.15338994089100
1.638-1.6760.1922160.15538634079100
1.676-1.7180.1742020.15938794081100
1.718-1.7640.1861930.15539334126100
1.764-1.8160.1721930.16438784071100
1.816-1.8750.192470.17738904137100
1.875-1.9420.1882180.16938574075100
1.942-2.020.1822430.16838674110100
2.02-2.1110.1571870.15639394126100
2.111-2.2230.1742330.15538804113100
2.223-2.3620.1921990.1673918411799
2.362-2.5440.1822100.17239434153100
2.544-2.80.192190.17739494168100
2.8-3.2050.22020.17639924194100
3.205-4.0360.1692230.1583931415498
4.036-29.6040.1592040.173926413093
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)
10.0740.14250.05670.29440.10410.24080.0193-0.037-0.02420.0275-0.0244-0.08720.02970.0337-0.00360.0111-0.0011-0.00150.0283-0.00690.0547-10.0127-12.262126.4119
20.1985-0.12420.05910.18170.17070.088-0.01780.00880.00080.0075-0.00230.01870.00180.00440.01820.0255-0.00310.00670.0183-0.00490.04-23.2237-19.297415.0585
30.1936-0.06670.1510.21570.20520.485-0.0266-0.0030.0362-0.0048-0.02510.0091-0.049-0.03390.04520.01950.001300.0141-0.00720.037-25.1854-4.756724.0904
40.2569-0.2524-0.24531.2136-0.01720.42250.10830.2755-0.17580.0554-0.08340.2168-0.0044-0.1470.04190.03970.0034-0.05750.0918-0.09190.1061-37.3739-31.7742-6.6148
50.6006-0.07010.03030.40.24740.20060.02680.1189-0.1208-0.0124-0.03580.05410.0064-0.00230.00560.0280.00680.00340.0471-0.03230.0416-22.7736-32.7674-0.9096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 1:47A1 - 47
2X-RAY DIFFRACTION2chain A and resseq 48:179A48 - 179
3X-RAY DIFFRACTION3chain A and resseq 180:313A180 - 313
4X-RAY DIFFRACTION4chain A and resseq 314:343A314 - 343
5X-RAY DIFFRACTION5chain A and resseq 344:461A344 - 461

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