+Open data
-Basic information
Entry | Database: PDB / ID: 7nyb | ||||||
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Title | TrmB complex with SAM | ||||||
Components | tRNA (guanine-N(7)-)-methyltransferase | ||||||
Keywords | RNA BINDING PROTEIN / m7G Methyltransferase / Rossman-like fold / tRNA modifying enzyme | ||||||
Function / homology | Function and homology information RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA methylation Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Blersch, K.F. / Ficner, R. / Neumann, P. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Rna Biol. / Year: 2021 Title: Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA. Authors: Blersch, K.F. / Burchert, J.P. / August, S.C. / Welp, L. / Neumann, P. / Koster, S. / Urlaub, H. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nyb.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nyb.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 7nyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/7nyb ftp://data.pdbj.org/pub/pdb/validation_reports/ny/7nyb | HTTPS FTP |
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-Related structure data
Related structure data | 7nziC 7nzjC 2fcaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 10 - 212 / Label seq-ID: 10 - 212
NCS oper:
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-Components
#1: Protein | Mass: 24537.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: trmB, ytmQ, BSU29900 / Production host: Escherichia coli (E. coli) References: UniProt: O34522, tRNA (guanine46-N7)-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 20%PEG4000, 20%Glycerol, 0.06M KAc, 0.08M (NH4)2SO4, 0.01M Triethylamine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2018 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→44.55 Å / Num. obs: 16092 / % possible obs: 99.9 % / Redundancy: 10.551 % / Biso Wilson estimate: 64.066 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.113 / Χ2: 0.897 / Net I/σ(I): 13.31 / Num. measured all: 169792 |
Reflection shell | Resolution: 2.45→2.5 Å / Redundancy: 10.808 % / Rmerge(I) obs: 1.307 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 939 / CC1/2: 0.746 / Rrim(I) all: 1.372 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FCA Resolution: 2.5→44.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2552 / WRfactor Rwork: 0.2099 / FOM work R set: 0.7625 / SU B: 12.786 / SU ML: 0.271 / SU R Cruickshank DPI: 1.1482 / SU Rfree: 0.3146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.148 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 182.69 Å2 / Biso mean: 66.423 Å2 / Biso min: 31.06 Å2
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Refinement step | Cycle: final / Resolution: 2.5→44.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 1641 / Type: TIGHT THERMAL / Rms dev position: 9.66 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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