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- PDB-7jlz: Crystal structure of 30S ribosomal A1408 methyltransferase from a... -

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Basic information

Entry
Database: PDB / ID: 7jlz
TitleCrystal structure of 30S ribosomal A1408 methyltransferase from an uncultured bacterium (UncKam)
Components16S rRNA methylase
KeywordsRNA BINDING PROTEIN / Ribosome methylation / Aminoglycoside resistance / A1408 methyltransferase
Function / homologytRNA (guanine(46)-N7)-methyltransferase activity / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 16S rRNA methylase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsNosrati, M. / 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: To be published
Title: Roles of conserved tryptophans in substrate recognition and catalysis by the aminoglycoside-resistance 16S rRNA (m1A1408) rRNA methyltransferases
Authors: Nosrati, M. / Witek, M.A. / Dayne, W. / Zelinskaya, N. / Dunham, C.M. / Conn, G.L.
History
DepositionJul 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8846
Polymers24,4041
Non-polymers4805
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.370, 66.330, 133.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-405-

SO4

21A-609-

HOH

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Components

#1: Protein 16S rRNA methylase


Mass: 24403.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: ACD_24C00409G0003 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K2DC64
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20-28% PEG 8000, 0.1M MES pH= 5.5-7.0, 0.2M Ammonium Sulfate
PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→40.115 Å / Num. obs: 27763 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 44.1 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.08242 / Rpim(I) all: 0.02637 / Rrim(I) all: 0.08674 / Net I/σ(I): 13.55
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 11.3 % / Num. unique obs: 2748 / CC1/2: 0.655 / CC star: 0.89 / Rpim(I) all: 0.6601 / % possible all: 99.78

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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: Swiss Model using 3MTE as template

3mte


Resolution: 1.64→40.11 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 1999 7.2 %
Rwork0.1962 25748 -
obs0.1982 27747 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.68 Å2 / Biso mean: 43.7607 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.64→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 25 126 1770
Biso mean--91.31 50.09 -
Num. residues----204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061681
X-RAY DIFFRACTIONf_angle_d0.8032274
X-RAY DIFFRACTIONf_chiral_restr0.055261
X-RAY DIFFRACTIONf_plane_restr0.006278
X-RAY DIFFRACTIONf_dihedral_angle_d14.3851022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.64-1.6810.36071440.36481850
1.681-1.72640.39481390.35911803
1.7264-1.77720.32731400.3151787
1.7772-1.83460.37211410.28821815
1.8346-1.90010.30981420.25071829
1.9001-1.97620.27691420.22861827
1.9762-2.06620.271410.21441820
2.0662-2.17510.25771420.22191818
2.1751-2.31130.24311420.20031831
2.3113-2.48980.24531420.20441829
2.4898-2.74030.24021430.20761841
2.7403-3.13670.26081440.2041857
3.1367-3.95130.21981450.16511875
3.9513-40.110.15911520.16991966
Refinement TLS params.Method: refined / Origin x: 66.6419 Å / Origin y: 70.3601 Å / Origin z: 16.9206 Å
111213212223313233
T0.2242 Å20.0138 Å2-0.0233 Å2-0.148 Å2-0.0301 Å2--0.2146 Å2
L2.1631 °2-1.2043 °20.3574 °2-2.1439 °2-0.2296 °2--2.7236 °2
S-0.1056 Å °-0.0725 Å °0.0169 Å °-0.1154 Å °0.0553 Å °0.1123 Å °-0.224 Å °-0.0982 Å °0.035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 212
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allA501 - 801
4X-RAY DIFFRACTION1allC1 - 126

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