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Yorodumi- PDB-8ad7: Flavin-dependent tryptophan 6-halogenase Thal in complex with D-Trp -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ad7 | ||||||
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Title | Flavin-dependent tryptophan 6-halogenase Thal in complex with D-Trp | ||||||
Components | Tryptophan 6-halogenase | ||||||
Keywords | FLAVOPROTEIN / halogenase / ThdH / D-amino acid / D-Trp unnatural substrate / tryptophan halogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces albogriseolus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Moritzer, A.C. / 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 | 8ad7.cif.gz | 226.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ad7.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ad7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ad7_validation.pdf.gz | 818.9 KB | Display | wwPDB validaton report |
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Full document | 8ad7_full_validation.pdf.gz | 828.1 KB | Display | |
Data in XML | 8ad7_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 8ad7_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/8ad7 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/8ad7 | HTTPS FTP |
-Related structure data
Related structure data | 8ad8C 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/951 / 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:
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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-DTR / | #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: 3.3 Å3/Da / Density % sol: 62.78 % / Description: HEXAGONAL PRISM |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: RESERVOIR: 0.1 M BICINE PH 8.2, 1.6 M K2HPO4/KH2PO4; PROTEIN CONCENTRATION: ~ 15 MG/ML; PROTEIN BUFFER: 10 MM TRIS PH 7.4, 50 MM NACL, 1 MM TCEP; PROTEIN AND SUBSTRATE D-TRP PREINCUBATED ...Details: RESERVOIR: 0.1 M BICINE PH 8.2, 1.6 M K2HPO4/KH2PO4; PROTEIN CONCENTRATION: ~ 15 MG/ML; PROTEIN BUFFER: 10 MM TRIS PH 7.4, 50 MM NACL, 1 MM TCEP; PROTEIN AND SUBSTRATE D-TRP PREINCUBATED BEFORE PLATE SET-UP; DROP RATIO: 1:1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9164 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9164 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→50 Å / Num. obs: 66588 / % possible obs: 100 % / Redundancy: 20.84 % / CC1/2: 0.998 / Rrim(I) all: 0.13 / Net I/σ(I): 14.09 |
Reflection shell | Resolution: 2.33→2.39 Å / Redundancy: 21.05 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 4908 / CC1/2: 0.746 / Rrim(I) all: 1.71 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H43 CHAINA Resolution: 2.33→49.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.301 / SU ML: 0.188 / Cross valid method: FREE R-VALUE / ESU R: 0.251 / ESU R Free: 0.208 Details: HYDROGENS HAVE BEEN ADDED IN THEIR 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→49.8 Å
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Refine LS restraints |
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