+Open data
-Basic information
Entry | Database: PDB / ID: 3x27 | ||||||
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Title | Structure of McbB in complex with tryptophan | ||||||
Components | Cucumopine synthase | ||||||
Keywords | LYASE / McbB / Pictet-Spenglerase | ||||||
Function / homology | Cucumopine synthase, C-terminal helical bundle domain / Cucumopine synthase C-terminal helical bundle domain / Cyclophilin - #20 / Cyclophilin / Beta Barrel / Mainly Beta / TRYPTOPHAN / Cucumopine synthase Function and homology information | ||||||
Biological species | Marinactinospora thermotolerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.481 Å | ||||||
Authors | Mori, T. / Sahashi, S. / Morita, H. / Abe, I. | ||||||
Citation | Journal: Chem.Biol. / Year: 2015 Title: Structural Basis for beta-Carboline Alkaloid Production by the Microbial Homodimeric Enzyme McbB Authors: Mori, T. / Hoshino, S. / Sahashi, S. / Wakimoto, T. / Matsui, T. / Morita, H. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x27.cif.gz | 260.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x27.ent.gz | 219.3 KB | Display | PDB format |
PDBx/mmJSON format | 3x27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/3x27 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/3x27 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38453.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinactinospora thermotolerans (bacteria) Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: R4QPW9 #2: Chemical | ChemComp-TRP / #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: 2.58 Å3/Da / Density % sol: 52.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM Tris-HCl, 18% PEG1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 17, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. obs: 56928 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 2.48→2.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.399 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.481→47.764 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 22.25 / Stereochemistry target values: MLHL
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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: 2.481→47.764 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: 20
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