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Yorodumi- PDB-4obv: Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (alpha-FMT) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4obv | ||||||
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Title | Ruminococcus gnavus tryptophan decarboxylase RUMGNA_01526 (alpha-FMT) | ||||||
Components | Pyridoxal-dependent decarboxylase domain protein | ||||||
Keywords | LYASE / Type 1 PLP-dependent / Decarboxylase | ||||||
Function / homology | Function and homology information L-tryptophan decarboxylase / L-tryptophan decarboxylase activity / tryptophan metabolic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Ruminococcus gnavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Fraser, J.S. / Van Benschoten, A.H. | ||||||
Citation | Journal: Cell Host Microbe / Year: 2014 Title: Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine. Authors: Williams, B.B. / Van Benschoten, A.H. / Cimermancic, P. / Donia, M.S. / Zimmermann, M. / Taketani, M. / Ishihara, A. / Kashyap, P.C. / Fraser, J.S. / Fischbach, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4obv.cif.gz | 370.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4obv.ent.gz | 305.7 KB | Display | PDB format |
PDBx/mmJSON format | 4obv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4obv ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4obv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 55024.621 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Gene: RUMGNA_01526 / Production host: Escherichia coli (E. coli) / References: UniProt: A7B1V0 #2: Chemical | ChemComp-2SU / #3: Chemical | ChemComp-3SO / { |
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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: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 30% ethoxyethanol, 0.1M citrate pH 5.25, 4% polypropylene P400, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2013 |
Radiation | Monochromator: Double flat crystal, Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→52.442 Å / Num. all: 55262 / Num. obs: 55229 / % possible obs: 99.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.84→2.991 Å / % possible all: 99.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→52.442 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→52.442 Å
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Refine LS restraints |
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LS refinement shell |
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