+Open data
-Basic information
Entry | Database: PDB / ID: 3vyw | |||||||||
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Title | Crystal structure of MNMC2 from Aquifex Aeolicus | |||||||||
Components | MNMC2 | |||||||||
Keywords | TRANSFERASE / tRNA wobble uridine / modification enzyme / genetic code / 5-methylaminomethyl-2-thiouridine / methyltransferase / 2-codon sets / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aquifex aeolicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.49 Å | |||||||||
Authors | Shibata, R. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1). Authors: Kitamura, A. / Nishimoto, M. / Sengoku, T. / Shibata, R. / Jager, G. / Bjork, G.R. / Grosjean, H. / Yokoyama, S. / Bessho, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vyw.cif.gz | 255.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vyw.ent.gz | 211 KB | Display | PDB format |
PDBx/mmJSON format | 3vyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vyw ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vyw | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 36188.395 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1980 / Plasmid: pET-11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: O67789 #2: Chemical | ChemComp-SAM / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 3350, sodium acetate, benzamidine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.49→45.39 Å / Num. obs: 47040 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 40.6 Å2 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 4689 / Rsym value: 0.295 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.49→45.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R: 1.042 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 51.096 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→45.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.489→2.554 Å / Total num. of bins used: 20
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