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Yorodumi- PDB-4bf9: Crystal structure of E. coli dihydrouridine synthase C (DusC) (se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bf9 | ||||||
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Title | Crystal structure of E. coli dihydrouridine synthase C (DusC) (selenomethionine derivative) | ||||||
Components | TRNA-DIHYDROURIDINE SYNTHASE C | ||||||
Keywords | OXIDOREDUCTASE / TRNA MODIFICATION | ||||||
Function / homology | Function and homology information tRNA-dihydrouridine16 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / FMN binding / flavin adenine dinucleotide binding / tRNA binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Model type details | P ATOMS ONLY, CHAIN B | ||||||
Authors | Byrne, R.T. / Whelan, F. / Konevega, A. / Aziz, N. / Rodnina, M. / Antson, A.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Major Reorientation of tRNA Substrates Defines Specificity of Dihydrouridine Synthases. Authors: Byrne, R.T. / Jenkins, H.T. / Peters, D.T. / Whelan, F. / Stowell, J. / Aziz, N. / Kasatsky, P. / Rodnina, M.V. / Koonin, E.V. / Konevega, A.L. / Antson, A.A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bf9.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bf9.ent.gz | 114.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bf9_validation.pdf.gz | 741 KB | Display | wwPDB validaton report |
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Full document | 4bf9_full_validation.pdf.gz | 741 KB | Display | |
Data in XML | 4bf9_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 4bf9_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bf9 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bf9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38076.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Strain: MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: P33371, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: MOLECULAR DIMENSIONS MORPHEUS SCREEN CONDITION D3, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9808 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9808 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→59.8 Å / Num. obs: 17124 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.6→58.17 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 15.027 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.164 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→58.17 Å
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Refine LS restraints |
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