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Yorodumi- PDB-6slt: Flavin-dependent tryptophan 6-halogenase Thal in complex with try... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6slt | ||||||
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Title | Flavin-dependent tryptophan 6-halogenase Thal in complex with tryptophan and FAD | ||||||
Components | Tryptophan 6-halogenase | ||||||
Keywords | FLAVOPROTEIN / tryptophan halogenase / ThdH / Thal / FAD / Tryptophan | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces albogriseolus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Moritzer, A. / Niemann, H.H. | ||||||
Citation | Journal: Protein Sci. / Year: 2019 Title: Binding of FAD and tryptophan to the tryptophan 6-halogenase Thal is negatively coupled. Authors: Moritzer, A.C. / Niemann, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6slt.cif.gz | 228.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6slt.ent.gz | 180.9 KB | Display | PDB format |
PDBx/mmJSON format | 6slt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/6slt ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6slt | HTTPS FTP |
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-Related structure data
Related structure data | 6slsC 6h43S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / 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: 0 / Auth seq-ID: 2 - 529 / Label seq-ID: 5 - 532
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60276.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thal, thdH / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1E280 |
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-Non-polymers , 6 types, 87 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-TRP / | #5: Chemical | ChemComp-AMP / | #6: Chemical | ChemComp-FAD / | #7: Water | ChemComp-HOH / | |
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-Details
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: 3.29 Å3/Da / Density % sol: 62.57 % / Description: hexagonal prism |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion / pH: 8.4 Details: reservoir: 0.1M bicine pH 8.4, 1.6M K2HPO4/KH2PO4 protein concentration: ~15mg/mL drop ratio: 2:1 (P:R) protein buffer: 10 mM Tris pH 8.4, 50 mM NaCl and 1 mM TCEP |
-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: 1 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 42328 / % possible obs: 100 % / Redundancy: 20.7 % / Biso Wilson estimate: 63.553 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.056 / Rrim(I) all: 0.181 / Net I/av σ(I): 14.6 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 20.4 % / Rmerge(I) obs: 1.696 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4441 / CC1/2: 0.775 / Rpim(I) all: 0.556 / Rrim(I) all: 1.785 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H43 Resolution: 2.7→49.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.11 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.647 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 181.07 Å2 / Biso mean: 69.882 Å2 / Biso min: 36.27 Å2
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Refinement step | Cycle: final / Resolution: 2.7→49.58 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16927 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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