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- PDB-6pqb: Crystal structure of aminoglycoside-resistance methyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 6pqb
TitleCrystal structure of aminoglycoside-resistance methyltransferase RmtC bound to S-adenosylhomocysteine (SAH)
Components16S rRNA (guanine(1405)-N(7))-methyltransferase
KeywordsTRANSFERASE / methyltransferase / ribosome / aminoglycoside resistance / S-adenosylhomocysteine
Function / homology16S rRNA (guanine1405-N7)-methyltransferase / Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria / Ribosomal RNA aminoglycoside-resistance methyltransferase / Ribosomal RNA methyltransferase (FmrO) / rRNA methyltransferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily / response to antibiotic / S-ADENOSYL-L-HOMOCYSTEINE / 16S rRNA (guanine(1405)-N(7))-methyltransferase
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsNosrati, M. / Hoffer, E.D. / Conn, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI088025 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Functionally critical residues in the aminoglycoside resistance-associated methyltransferase RmtC play distinct roles in 30S substrate recognition.
Authors: Nosrati, M. / Dey, D. / Mehrani, A. / Strassler, S.E. / Zelinskaya, N. / Hoffer, E.D. / Stagg, S.M. / Dunham, C.M. / Conn, G.L.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _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
B: 16S rRNA (guanine(1405)-N(7))-methyltransferase
C: 16S rRNA (guanine(1405)-N(7))-methyltransferase
D: 16S rRNA (guanine(1405)-N(7))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7018
Polymers129,1644
Non-polymers1,5384
Water1629
1
A: 16S rRNA (guanine(1405)-N(7))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6752
Polymers32,2911
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 16S rRNA (guanine(1405)-N(7))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6752
Polymers32,2911
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 16S rRNA (guanine(1405)-N(7))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6752
Polymers32,2911
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 16S rRNA (guanine(1405)-N(7))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6752
Polymers32,2911
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.540, 163.540, 122.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
16S rRNA (guanine(1405)-N(7))-methyltransferase / 16S rRNA m7G1405 methyltransferase


Mass: 32290.963 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: rmtC / Plasmid: pET44 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q33DX5, 16S rRNA (guanine1405-N7)-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M ammonium sulfate, 0.1 M Na HEPES pH 7.0, 3 mM mellitic acid
PH range: 6.8-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.14→41 Å / Num. obs: 32552 / % possible obs: 100 % / Redundancy: 8.7 % / CC1/2: 0.99 / Rpim(I) all: 0.047 / Net I/σ(I): 10.82
Reflection shellResolution: 3.14→3.25 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 3224 / CC1/2: 0.419 / Rpim(I) all: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CN0

6cn0


Resolution: 3.14→40.885 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.25
RfactorNum. reflection% reflection
Rfree0.2326 1669 5.13 %
Rwork0.2002 --
obs0.2018 32552 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 256.43 Å2 / Biso mean: 134.1971 Å2 / Biso min: 68.36 Å2
Refinement stepCycle: final / Resolution: 3.14→40.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8530 0 104 9 8643
Biso mean--111.64 91.39 -
Num. residues----1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028806
X-RAY DIFFRACTIONf_angle_d0.47411879
X-RAY DIFFRACTIONf_chiral_restr0.0391339
X-RAY DIFFRACTIONf_plane_restr0.0051494
X-RAY DIFFRACTIONf_dihedral_angle_d12.2545400
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1401-3.23250.41251290.35822568100
3.2325-3.33670.39691380.32582553100
3.3367-3.45590.30111430.29482564100
3.4559-3.59420.2911120.24972584100
3.5942-3.75770.29031290.24072556100
3.7577-3.95570.25751310.19782582100
3.9557-4.20330.22181730.17212543100
4.2033-4.52740.19451580.15852567100
4.5274-4.98230.17041700.15522541100
4.9823-5.70160.25131200.18622588100
5.7016-7.17710.22061550.2352588100
7.1771-40.8850.22881110.1854264999
Refinement TLS params.Method: refined / Origin x: 136.1806 Å / Origin y: 124.3803 Å / Origin z: 23.0524 Å
111213212223313233
T0.7763 Å2-0.0281 Å2-0.0348 Å2-0.8645 Å2-0.0382 Å2--0.9521 Å2
L0.8397 °20.615 °20.4537 °2-0.6461 °20.2001 °2--0.6218 °2
S0.0122 Å °0.1424 Å °-0.1673 Å °0.1004 Å °0.014 Å °-0.0338 Å °-0.0091 Å °0.2051 Å °-0.0307 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 301
2X-RAY DIFFRACTION1allB3 - 301
3X-RAY DIFFRACTION1allC3 - 301
4X-RAY DIFFRACTION1allD3 - 301
5X-RAY DIFFRACTION1allE1 - 9

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