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Yorodumi- PDB-3u4d: Crystal structure of YwfH, NADPH dependent reductase involved in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u4d | ||||||
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Title | Crystal structure of YwfH, NADPH dependent reductase involved in Bacilysin biosynthesis | ||||||
Components | Bacilysin biosynthesis oxidoreductase ywfH | ||||||
Keywords | OXIDOREDUCTASE / NADPH binding motif / Rossmann fold / SDR superfamily / Bacilysin biosynthesis | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / antibiotic biosynthetic process / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Rajavel, M. / Gopal, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural insights into the role of Bacillus subtilis YwfH (BacG) in tetrahydrotyrosine synthesis Authors: Rajavel, M. / Perinbam, K. / Gopal, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u4d.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u4d.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 3u4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/3u4d ftp://data.pdbj.org/pub/pdb/validation_reports/u4/3u4d | HTTPS FTP |
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-Related structure data
Related structure data | 3u49C 3u4cSC C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 30465.623 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU37680, ipa-86r, ywfH / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P39644 |
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#2: 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: 2.34 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 0.1M HEPES, 1.4M Tri-sodium citrate dihydrate, pH 7.5, Microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 2, 2011 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→28.71 Å / Num. all: 8750 / Num. obs: 8551 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5 / Redundancy: 11.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.9 / Num. unique all: 331 / % possible all: 79.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U4C Resolution: 2.7→28.71 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.7695 / SU ML: 0.38 / σ(F): 0 / Phase error: 27.69 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.888 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 294.11 Å2 / Biso mean: 81.7782 Å2 / Biso min: 29.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→28.71 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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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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