+Open data
-Basic information
Entry | Database: PDB / ID: 8fov | ||||||
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Title | AbeH (Tryptophan-5-halogenase) bound to FAD and Cl | ||||||
Components | Tryptophan 5-halogenase | ||||||
Keywords | OXIDOREDUCTASE / halogenase / flavin | ||||||
Function / homology | Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / nucleotide binding / ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 5-halogenase Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å | ||||||
Authors | Ashaduzzaman, M. / Bellizzi, J.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biorxiv / Year: 2023 Title: Crystallographic and thermodynamic evidence of negative cooperativity of flavin and tryptophan binding in the flavin-dependent halogenases AbeH and BorH. Authors: Ashaduzzaman, M. / Lingkon, K. / De Silva, A.J. / Bellizzi, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fov.cif.gz | 448 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fov.ent.gz | 349 KB | Display | PDB format |
PDBx/mmJSON format | 8fov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fov_validation.pdf.gz | 939.9 KB | Display | wwPDB validaton report |
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Full document | 8fov_full_validation.pdf.gz | 945.3 KB | Display | |
Data in XML | 8fov_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 8fov_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/8fov ftp://data.pdbj.org/pub/pdb/validation_reports/fo/8fov | HTTPS FTP |
-Related structure data
Related structure data | 8foxC 8ttiC 8ttjC 8ttkC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58350.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Contains extra Proline at N-terminus (residue 0) remaining from cleavage of linker with N-terminal His-tag. Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: abeH / Production host: Escherichia coli (E. coli) / References: UniProt: F6LWA5 |
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-Non-polymers , 5 types, 825 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / #6: 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: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Drop:1:1 ratio of reservoir solution and (50uM AbeH/25 mM FAD in 20 mM HEPES pH 7.2 and 35 mM sodium citrate); Reservoir (500 uL): 0.1 M Bis-Tris pH 6.2, 0.2 M magnesium acetate, 11% (v/v) PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→56.14 Å / Num. obs: 93637 / % possible obs: 99.63 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.06443 / Rpim(I) all: 0.06443 / Rrim(I) all: 0.09112 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.86→1.926 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3797 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 9276 / CC1/2: 0.708 / CC star: 0.911 / Rpim(I) all: 0.3797 / Rrim(I) all: 0.537 / % possible all: 99.96 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→56.14 Å / SU ML: 0.1911 / Cross valid method: FREE R-VALUE / σ(F): 0.6 / Phase error: 20.1232 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 29.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→56.14 Å
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Refine LS restraints |
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LS refinement shell |
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