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Yorodumi- PDB-8ad8: Flavin-dependent tryptophan 6-halogenase Thal in complex with a D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ad8 | ||||||
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Title | Flavin-dependent tryptophan 6-halogenase Thal in complex with a D-Trp-Ser dipeptide | ||||||
Components | Tryptophan 6-halogenase | ||||||
Keywords | FLAVOPROTEIN / halogenase / ThdH / dipeptide / unnatural substrate / tryptophan halogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces albogriseolus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Gafe, S. / Moritzer, A.C. / Montua, N. / Sewald, N. / Niemann, H.H. | ||||||
Funding support | 1items
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Citation | Journal: Chembiochem / Year: 2023 Title: Enzymatic Late-Stage Halogenation of Peptides. Authors: Schnepel, C. / Moritzer, A.C. / Gafe, S. / Montua, N. / Minges, H. / Niess, A. / Niemann, H.H. / Sewald, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ad8.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ad8.ent.gz | 173.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ad8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ad8_validation.pdf.gz | 746 KB | Display | wwPDB validaton report |
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Full document | 8ad8_full_validation.pdf.gz | 754 KB | Display | |
Data in XML | 8ad8_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 8ad8_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/8ad8 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/8ad8 | HTTPS FTP |
-Related structure data
Related structure data | 8ad7C 6h43S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/952 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 2 - 529 / Label seq-ID: 5 - 532
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-Components
#1: Protein | Mass: 60276.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal residues GAMG remain after TEV cleavage of the N-terminal His6-tag Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal, thdH / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280 #2: Chemical | #3: Chemical | ChemComp-LT0 / | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.25 Å3/Da / Density % sol: 62.16 % / Description: hexagonal prism |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: Reservoir solution: 100 mM Bicine pH 9.0, 1.6 M KH2PO4/K2HPO4; Protein concentration: 15 mg/ml; Protein buffer: 10 mM Tris pH 7.4, 50 mM NaCl, 1 mM DTT; Drop ratio: 1:1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→47.98 Å / Num. obs: 32396 / % possible obs: 100 % / Redundancy: 10.54 % / Biso Wilson estimate: 69 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.154 / Net I/σ(I): 16.71 |
Reflection shell | Resolution: 2.95→3.03 Å / Redundancy: 11.03 % / Mean I/σ(I) obs: 1.99 / Num. unique obs: 2386 / CC1/2: 0.676 / Rrim(I) all: 1.54 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H43 Resolution: 2.95→47.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.589 / SU ML: 0.329 / Cross valid method: FREE R-VALUE / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 70.78 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→47.98 Å
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Refine LS restraints |
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