+Open data
-Basic information
Entry | Database: PDB / ID: 4ntc | ||||||
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Title | Crystal structure of GliT | ||||||
Components | GliT | ||||||
Keywords | OXIDOREDUCTASE / disulfide bond / epipolythiodioxopiperazine / gliotoxin / natural sulfur products | ||||||
Function / homology | Function and homology information gliotoxin biosynthetic process / Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / mycotoxin biosynthetic process / cellular response to mycotoxin / : / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Scharf, D.H. / Groll, M. / Habel, A. / Heinekamp, T. / Hertweck, C. / Brakhage, A.A. / Huber, E.M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Flavoenzyme-Catalyzed Formation of Disulfide Bonds in Natural Products Authors: Scharf, D.H. / Groll, M. / Habel, A. / Heinekamp, T. / Hertweck, C. / Brakhage, A.A. / Huber, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ntc.cif.gz | 267.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ntc.ent.gz | 215 KB | Display | PDB format |
PDBx/mmJSON format | 4ntc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/4ntc ftp://data.pdbj.org/pub/pdb/validation_reports/nt/4ntc | HTTPS FTP |
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-Related structure data
Related structure data | 4ntdC 4nteC 3fbsS S: Starting model for refinement 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 36126.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: deltaakuB / Gene: gliT / Plasmid: pET43.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5MBU7, UniProt: E9RAH5*PLUS #2: Chemical | #3: 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: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M tri-Na citrate, 20% PEG3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2012 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 54166 / Num. obs: 51186 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.3 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FBS Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.258 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.627 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 28.882 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.948 Å / Total num. of bins used: 20
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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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