+Open data
-Basic information
Entry | Database: PDB / ID: 4z43 | ||||||
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Title | Crystal structure of Tryptophan 7-halogenase (PrnA) Mutant E450K | ||||||
Components | Flavin-dependent tryptophan halogenase PrnA | ||||||
Keywords | OXIDOREDUCTASE / 7-halogenase (PrnA) Mutant E450K | ||||||
Function / homology | Function and homology information tryptophan 7-halogenase / antibiotic biosynthetic process / monooxygenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Levy, C.W. | ||||||
Citation | Journal: Chem Sci / Year: 2015 Title: Extending the biocatalytic scope of regiocomplementary flavin-dependent halogenase enzymes. Authors: Shepherd, S.A. / Karthikeyan, C. / Latham, J. / Struck, A.W. / Thompson, M.L. / Menon, B.R.K. / Styles, M.Q. / Levy, C. / Leys, D. / Micklefield, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z43.cif.gz | 220.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z43.ent.gz | 177 KB | Display | PDB format |
PDBx/mmJSON format | 4z43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z43_validation.pdf.gz | 717.2 KB | Display | wwPDB validaton report |
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Full document | 4z43_full_validation.pdf.gz | 727.2 KB | Display | |
Data in XML | 4z43_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 4z43_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/4z43 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/4z43 | HTTPS FTP |
-Related structure data
Related structure data | 4z44C 2aqjS 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
#1: Protein | Mass: 61146.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: prnA / Production host: Escherichia coli (E. coli) / References: UniProt: P95480, tryptophan 7-halogenase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 1.0 M Imidazole and MES Buffer Mix at pH 6.5, containing 0.09 M nitrate phosphate sulfate salt mix (NaNO3; Na2HPO4; (NH4)2SO4)) and 60% w/v glycerol and polyethylene glycol 4K) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9779 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→30.85 Å / Num. obs: 30949 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.16 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.44 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AQJ Resolution: 2.29→30.85 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.22 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→30.85 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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