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Yorodumi- PDB-7ctq: Peptidyl tryptophan dihydroxylase QhpG essential for tryptophylqu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ctq | ||||||||||||||||||
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Title | Peptidyl tryptophan dihydroxylase QhpG essential for tryptophylquinone cofactor biogenesis | ||||||||||||||||||
Components | Peptidyl tryptophan dihydroxylase | ||||||||||||||||||
Keywords | FLAVOPROTEIN / FAD-dependent monooxygenase / Cofactor biogenesis / Cysteine tryptophylquinone / Quinohemoprotein amine dehydrogenase | ||||||||||||||||||
Function / homology | Flavin-dependent halogenase / Tryptophan halogenase / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Chem-GKC / HEXANE-1,6-DIOL / FAD-dependent oxidoreductase Function and homology information | ||||||||||||||||||
Biological species | Pseudomonas putida (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.978 Å | ||||||||||||||||||
Authors | Oozeki, T. / Nakai, T. / Okajima, T. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: Nat Commun / Year: 2021 Title: Functional and structural characterization of a flavoprotein monooxygenase essential for biogenesis of tryptophylquinone cofactor. Authors: Oozeki, T. / Nakai, T. / Kozakai, K. / Okamoto, K. / Kuroda, S. / Kobayashi, K. / Tanizawa, K. / Okajima, T. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ctq.cif.gz | 197.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ctq.ent.gz | 154.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ctq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ctq_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7ctq_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ctq_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 7ctq_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/7ctq ftp://data.pdbj.org/pub/pdb/validation_reports/ct/7ctq | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47252.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GB LC575123 / Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: NBRC 15366 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A1L5PQA4*PLUS #2: Chemical | #3: Chemical | ChemComp-HEZ / #4: Chemical | ChemComp-GKC / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | LC575123 | |
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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: 2.44 Å3/Da / Density % sol: 49.51 % |
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Crystal grow | Temperature: 277.2 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM HEPES (pH 7.0), 20 mM MgCl2, 17% (v/v) Poly(acrylic acid sodium salt) 5100, 1.8% (w/v) 1,6-hexanediol, 34 mM Cyclohexyl-methyl-beta-D-maltoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.978→37.758 Å / Num. obs: 63162 / % possible obs: 98.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.978→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 19439 / CC1/2: 0.801 / Rrim(I) all: 0.625 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.978→37.758 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.01 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.58 Å2 / Biso mean: 45.162 Å2 / Biso min: 16.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.978→37.758 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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