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- PDB-3m6x: Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 3m6x
TitleMulti-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P21212
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 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Sun protein; domain 3 / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase ...: / 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 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Sun protein; domain 3 / 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
Ribosomal RNA small subunit methyltransferase F
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.676 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: 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
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1462
Polymers51,1101
Non-polymers351
Water11,980665
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)102,2914
Polymers102,2202
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1800 Å2
ΔGint-26 kcal/mol
Surface area36630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.786, 109.093, 50.800
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-548-

HOH

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Components

#1: Protein rRNA methylase


Mass: 51110.168 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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 8.5
Details: 160 mM Magnesium chloride hexahydrate, 80 mM TRIS-HCl (pH 8.5) and 24 % w/v PEG4000, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2008 / Details: Slits: Variable vertical and horizontal slits
RadiationMonochromator: System consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. ...Monochromator: System consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionRedundancy: 6.4 % / Av σ(I) over netI: 14.24 / Number: 706932 / Rmerge(I) obs: 0.15 / Χ2: 1.01 / D res high: 1.68 Å / D res low: 30 Å / Num. obs: 110000 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.623099.910.0991.6197.3
2.873.6210010.1241.3937.5
2.512.8710010.1621.0747.6
2.282.5110010.1921.0867.3
2.122.2810010.2321.0946.8
1.992.1210010.240.8146.6
1.891.9999.910.3190.8236.3
1.811.8999.610.3860.5865.9
1.741.819910.4350.5315.1
1.681.7497.810.4870.4833.9
ReflectionResolution: 1.68→30 Å / Num. obs: 110000 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.15 / Χ2: 1.012 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.68-1.743.90.487108430.48397.8
1.74-1.815.10.435109370.53199
1.81-1.895.90.386109480.58699.6
1.89-1.996.30.319110420.82399.9
1.99-2.126.60.24110760.814100
2.12-2.286.80.232109881.094100
2.28-2.517.30.192110411.086100
2.51-2.877.60.162110381.074100
2.87-3.627.50.124110341.393100
3.62-307.30.099110531.61999.9

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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: 1.676→29.569 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.895 / SU ML: 0.21 / σ(F): 0.76 / Phase error: 17.86 / Stereochemistry target values: ML
Details: ANOMALOUS SCATTERER GROUPS DETAILS. NUMBER OF ANOMALOUS SCATTERER GROUPS : 1 ANOMALOUS SCATTERER GROUP : 1 SELECTION: name SE fp : -8.0000 fdp : 5.6051
RfactorNum. reflection% reflection
Rfree0.192 5569 5.09 %
Rwork0.173 --
obs0.174 109375 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.533 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 82.12 Å2 / Biso mean: 19.774 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.319 Å20 Å20 Å2
2--0.326 Å20 Å2
3---1.993 Å2
Refinement stepCycle: LAST / Resolution: 1.676→29.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 1 665 4223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043684
X-RAY DIFFRACTIONf_angle_d0.9365011
X-RAY DIFFRACTIONf_chiral_restr0.061523
X-RAY DIFFRACTIONf_plane_restr0.005665
X-RAY DIFFRACTIONf_dihedral_angle_d17.411379
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 (%)
1.676-1.6950.2661600.2173084324487
1.695-1.7150.2381870.2053410359799
1.715-1.7360.2051700.1953445361598
1.736-1.7580.2371810.1853457363898
1.758-1.7810.2062050.1823420362599
1.781-1.8050.2421940.1763491368599
1.805-1.8310.2111610.1743523368499
1.831-1.8590.2151580.16934513609100
1.859-1.8880.1951760.1813522369899
1.888-1.9180.2251720.1793429360199
1.918-1.9520.1952240.1783483370799
1.952-1.9870.2061670.1663434360199
1.987-2.0250.1882110.16235053716100
2.025-2.0670.2031960.15934353631100
2.067-2.1120.191650.15135403705100
2.112-2.1610.1721810.15734693650100
2.161-2.2150.1982090.1623471368098
2.215-2.2740.21780.1753438361699
2.274-2.3410.2151840.1683402358697
2.341-2.4170.1972070.16834973704100
2.417-2.5030.1772090.16834393648100
2.503-2.6030.191810.1763477365899
2.603-2.7220.1721580.1735253683100
2.722-2.8650.2231680.17235253693100
2.865-3.0450.1731870.17434873674100
3.045-3.2790.1962060.17134763682100
3.279-3.6090.1551700.15835253695100
3.609-4.130.1632250.14434503675100
4.13-5.1990.161920.14235143706100
5.199-29.5740.1631870.17834823669100
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)
10.02940.15570.02910.77330.14080.12060.0013-0.01690.0001-0.0016-0.0034-0.1524-0.00230.0414-0.0027-0.0074-0.00220.00190.017-0.01240.0582-9.8797-11.54326.615
20.2036-0.11790.02160.21290.10120.1207-0.0290.00940.00120.00390.0030.0459-0.00690.01510.0238-0.00230.00970.014-0.0253-0.01950.0024-23.237-19.346215.0158
30.20360.0030.18560.1250.13660.4428-0.0270.01480.0248-0.0012-0.02470.0045-0.0475-0.00670.04590.06520.0067-0.00120.0569-0.00830.0834-25.1742-4.792623.9417
40.3377-0.64690.11781.51940.20610.70540.10710.1425-0.2155-0.0196-0.16390.2551-0.0075-0.01330.05890.02030.0027-0.040.0725-0.06850.116-37.4267-31.7759-6.5885
50.6044-0.17180.07780.31730.15720.1310.02280.1175-0.1091-0.0085-0.02490.034-0.00360.0219-0.00290.00760.00980.00440.0194-0.03370.0187-22.812-32.8739-0.9003
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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