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Yorodumi- PDB-5b4e: Sulfur Transferase TtuA in complex with iron sulfur cluster and A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b4e | ||||||
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Title | Sulfur Transferase TtuA in complex with iron sulfur cluster and ATP derivative | ||||||
Components | Sulfur Transferase TtuA | ||||||
Keywords | TRANSFERASE / sulfur transferase | ||||||
Function / homology | Function and homology information tRNA-5-methyluridine54 2-sulfurtransferase / tRNA thio-modification / tRNA wobble uridine modification / 4 iron, 4 sulfur cluster binding / transferase activity / tRNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.698 Å | ||||||
Authors | Chen, M. / Narai, S. / Tanaka, Y. / Yao, M. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA Authors: Chen, M. / Asai, S.I. / Narai, S. / Nambu, S. / Omura, N. / Sakaguchi, Y. / Suzuki, T. / Ikeda-Saito, M. / Watanabe, K. / Yao, M. / Shigi, N. / Tanaka, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b4e.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b4e.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 5b4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/5b4e ftp://data.pdbj.org/pub/pdb/validation_reports/b4/5b4e | HTTPS FTP |
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-Related structure data
Related structure data | 5b4fC 5ghaC 5b4g 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37309.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C0106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72LF3 |
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-Non-polymers , 6 types, 50 molecules
#2: Chemical | #3: Chemical | ChemComp-ANP / | #4: Chemical | ChemComp-SF4 / | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-IPA / | #7: Water | ChemComp-HOH / | |
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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: 4.46 Å3/Da / Density % sol: 72.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate (pH 3.8-5.6), 30-60%(v/v) 1,2-propanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.35 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.35 Å / Relative weight: 1 |
Reflection | Resolution: 2.698→46.5 Å / Num. obs: 35452 / % possible obs: 99.8 % / Redundancy: 7.74 % / Rsym value: 0.086 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.698→2.86 Å / Redundancy: 7.62 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 2.74 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Resolution: 2.698→46.455 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.79 Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.698→46.455 Å
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Refine LS restraints |
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LS refinement shell |
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