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- PDB-6pi9: Crystal structure of 16S rRNA methyltransferase RmtF in complex w... -

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Basic information

Entry
Database: PDB / ID: 6pi9
TitleCrystal structure of 16S rRNA methyltransferase RmtF in complex with S-Adenosyl-L-homocysteine
Components16S rRNA (guanine(1405)-N(7))-methyltransferase
KeywordsTRANSFERASE / methyltransferase domain / methyltransferase / plasmid / 16S rRNA / antibiotic resistance / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


16S rRNA (guanine1405-N7)-methyltransferase / rRNA methyltransferase activity / response to antibiotic
Similarity search - Function
Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria / Ribosomal RNA aminoglycoside-resistance methyltransferase / Ribosomal RNA methyltransferase (FmrO) / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria / Ribosomal RNA aminoglycoside-resistance methyltransferase / Ribosomal RNA methyltransferase (FmrO) / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / 16S rRNA (guanine(1405)-N(7))-methyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStogios, P.J. / Kim, Y. / Evdokimova, E. / Di Leo, R. / Semper, C. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To be Published
Title: Crystal structure of 16S rRNA methylase RmtF in complex with S-Adenosyl-L-homocysteine
Authors: Stogios, P.J.
History
DepositionJun 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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: 16S rRNA (guanine(1405)-N(7))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1452
Polymers28,7601
Non-polymers3841
Water3,513195
1
A: 16S rRNA (guanine(1405)-N(7))-methyltransferase
hetero molecules

A: 16S rRNA (guanine(1405)-N(7))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2894
Polymers57,5212
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area3370 Å2
ΔGint-19 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.637, 77.637, 96.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

21A-588-

HOH

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Components

#1: Protein 16S rRNA (guanine(1405)-N(7))-methyltransferase / RmtF


Mass: 28760.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: rmtF, pN11x00042NDM_104 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)Gold
References: UniProt: I1YZZ5, 16S rRNA (guanine1405-N7)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 3.5 M sodium formate, 0.1 M sodium acetate, pH 4.8, 2 mM S-adenosyl-L-methionine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 26247 / % possible obs: 99.8 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Net I/σ(I): 41.08
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.626 / Num. unique obs: 1291 / CC1/2: 0.546 / Rpim(I) all: 0.489 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.15_3448: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FRH

3frh


Resolution: 1.85→29.829 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1295 5 %RANDOM
Rwork0.1918 ---
obs0.194 25918 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→29.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 26 195 2235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142115
X-RAY DIFFRACTIONf_angle_d1.3882870
X-RAY DIFFRACTIONf_dihedral_angle_d21.565815
X-RAY DIFFRACTIONf_chiral_restr0.094328
X-RAY DIFFRACTIONf_plane_restr0.009372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.92410.35331400.31212658X-RAY DIFFRACTION100
1.9241-2.01170.28961420.23922696X-RAY DIFFRACTION100
2.0117-2.11770.2671410.21762688X-RAY DIFFRACTION100
2.1177-2.25030.25641420.21242693X-RAY DIFFRACTION100
2.2503-2.4240.27341440.20312727X-RAY DIFFRACTION100
2.424-2.66780.25421410.21382702X-RAY DIFFRACTION100
2.6678-3.05350.23881450.21652746X-RAY DIFFRACTION100
3.0535-3.84580.25211470.18012777X-RAY DIFFRACTION100
3.8458-29.83270.20231530.16852936X-RAY DIFFRACTION100
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)
12.95931.62390.37411.4614-1.03142.9246-0.21990.44910.2702-0.25660.2821-0.35270.17480.53470.01340.2676-0.0146-0.03450.75310.08660.36462.1294-26.0622-12.1868
20.6905-0.41290.17771.69350.43570.4448-0.33990.2081-0.1791-0.10890.1167-0.07110.48750.463-0.0120.3432-0.05620.02870.6416-0.0360.307-3.6803-33.7082-13.5562
32.5855-1.2011-1.92110.931.04892.6540.58151.03960.7309-0.7704-0.1066-0.1025-1.2220.10430.09330.3472-0.0201-0.07180.6581-0.00580.3613-7.6115-26.7631-16.3134
42.46730.31161.78061.01510.09552.9433-0.47060.10111.7599-0.4888-0.08570.2892-1.33120.4271-0.11120.6537-0.0003-0.0960.6388-0.03541.0544-19.0799-10.3053.3582
50.340.0039-0.04560.4379-0.31040.16760.0799-1.03841.11210.4762-0.1997-0.1878-0.6585-0.3590.00090.34140.0156-0.06050.7756-0.16520.408-17.8823-21.882911.7035
66.75410.31471.36641.68541.23893.0318-0.06-0.80730.48110.19510.0953-0.0640.06150.2675-0.01530.22350.0392-0.01390.4746-0.04890.2742-15.4672-24.4416.8701
71.49240.28070.16320.66850.6621.37650.04180.27260.3694-0.0635-0.01460.8568-0.732-0.1543-00.3974-0.0011-0.03140.41820.02850.4871-32.1896-28.322-7.1681
83.34150.49630.62742.2762.62722.9105-0.1402-1.08290.12930.51170.03980.26730.17-0.8951-0.00040.27540.00950.04860.63370.0330.3922-31.1432-29.83196.6585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 110 )
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 213 )
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 235 )
8X-RAY DIFFRACTION8chain 'A' and (resid 236 through 259 )

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