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Yorodumi- PDB-8h27: Crystal structure of MnmM from S. aureus complexed with SAM (2.04 A) -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h27 | ||||||
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Title | Crystal structure of MnmM from S. aureus complexed with SAM (2.04 A) | ||||||
Components | 16S rRNA (Cytosine(1402)-N(4))-methyltransferase | ||||||
Keywords | TRANSFERASE / Methyltrnasferase tRNA post-transcriptional modification MnmC mnm5(s2)U | ||||||
Function / homology | tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / Putative rRNA methylase / Putative rRNA methylase / tRNA processing / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / tRNA (mnm(5)s(2)U34)-methyltransferase Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Kim, J. / Cho, G. / Lee, J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification. Authors: Cho, G. / Lee, J. / Kim, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h27.cif.gz | 299.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h27.ent.gz | 244.1 KB | Display | PDB format |
PDBx/mmJSON format | 8h27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h27_validation.pdf.gz | 703.9 KB | Display | wwPDB validaton report |
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Full document | 8h27_full_validation.pdf.gz | 710.5 KB | Display | |
Data in XML | 8h27_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 8h27_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/8h27 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/8h27 | HTTPS FTP |
-Related structure data
Related structure data | 8h0sC 8h0tC 8h1aC 8h1bC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21964.928 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01878 / Plasmid: pLATE31 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FXG9 #2: Chemical | ChemComp-SAM / | #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: 2.69 Å3/Da / Density % sol: 54.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, and 25% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→43.46 Å / Num. obs: 46406 / % possible obs: 84.6 % / Redundancy: 13.9 % / Biso Wilson estimate: 40.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.03 / Rrim(I) all: 0.112 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.04→2.23 Å / Redundancy: 14.6 % / Rmerge(I) obs: 2.271 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4642 / CC1/2: 0.627 / Rpim(I) all: 0.615 / Rrim(I) all: 2.353 / % possible all: 36.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold model (UniProt: Q2FXG9) Resolution: 2.04→43.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.812 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.712 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→43.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.041→2.094 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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