[English] 日本語
Yorodumi- PDB-3fpz: Saccharomyces cerevisiae THI4p is a suicide thiamin thiazole synthase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fpz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Saccharomyces cerevisiae THI4p is a suicide thiamin thiazole synthase | |||||||||
Components | Thiazole biosynthetic enzyme | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Thiazole biosynthetic enzyme in yeast / FAD / Mitochondrion / NAD / Thiamine biosynthesis / Transit peptide | |||||||||
Function / homology | Function and homology information cysteine-dependent adenosine diphosphate thiazole synthase / thiazole biosynthetic process / pentosyltransferase activity / thiamine biosynthetic process / mitochondrial genome maintenance / ferrous iron binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å | |||||||||
Authors | Bale, S. / Chatterjee, A. / Dorrestein, P.C. / Begley, T.P. / Ealick, S.E. | |||||||||
Citation | Journal: Nature / Year: 2011 Title: Saccharomyces cerevisiae THI4p is a suicide thiamine thiazole synthase. Authors: Chatterjee, A. / Abeydeera, N.D. / Bale, S. / Pai, P.J. / Dorrestein, P.C. / Russell, D.H. / Ealick, S.E. / Begley, T.P. #1: Journal: Biochemistry / Year: 2006 Title: Structural insights into the function of the thiamin biosynthetic enzyme Thi4 from Saccharomyces cerevisiae. Authors: Jurgenson, C.T. / Chatterjee, A. / Begley, T.P. / Ealick, S.E. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fpz.cif.gz | 143.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fpz.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 3fpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/3fpz ftp://data.pdbj.org/pub/pdb/validation_reports/fp/3fpz | HTTPS FTP |
---|
-Related structure data
Related structure data | 1rp0S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 16 - 326 / Label seq-ID: 16 - 326
|
-Components
#1: Protein | Mass: 34995.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: THI4, ESP35, MOL1, YGR144W, G6620 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P32318 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE FORMATION OF DHA FROM CYS IS DUE TO THE REACTION CATALYZED BY THE ENZYME. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.55 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.65-2.00 M Li2SO4, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9831 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9831 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. all: 63286 / Num. obs: 63274 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Χ2: 0.96 / Net I/σ(I): 22.669 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6023 / Rsym value: 0.256 / Χ2: 0.803 / % possible all: 94 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB entry 1RP0 Resolution: 1.82→49.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.694 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 93.97 Å2 / Biso mean: 28.26 Å2 / Biso min: 12.23 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→49.75 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2306 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.822→1.869 Å / Total num. of bins used: 20
|