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Yorodumi- PDB-2ar8: The structure of tryptophan 7-halogenase (PrnA)suggests a mechani... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ar8 | ||||||
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Title | The structure of tryptophan 7-halogenase (PrnA)suggests a mechanism for regioselective chlorination | ||||||
Components | tryptophan halogenase PrnA | ||||||
Keywords | BIOSYNTHETIC PROTEIN / tryptophan 7-halogenase / flavin-dependent halogenase / helical bundle / sandwiched sheets / Structural Genomics / Scottish Structural Proteomics Facility / SSPF | ||||||
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: 2.2 Å | ||||||
Authors | Dong, C. / Flecks, S. / Unversucht, S. / Haupt, C. / Van Pee, K.H. / Naismith, J.H. / Scottish Structural Proteomics Facility (SSPF) | ||||||
Citation | Journal: Science / Year: 2005 Title: Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination. Authors: Dong, C. / Flecks, S. / Unversucht, S. / Haupt, C. / van Pee, K.H. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and X-ray diffraction of a halogenating enzyme, tryptophan 7-halogenase, from Pseudomonas fluorescens Authors: Dong, C. / Kotzsch, A. / Dorward, M. / Van Pee, K.H. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ar8.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ar8.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ar8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ar8_validation.pdf.gz | 724.8 KB | Display | wwPDB validaton report |
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Full document | 2ar8_full_validation.pdf.gz | 728.4 KB | Display | |
Data in XML | 2ar8_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 2ar8_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/2ar8 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/2ar8 | HTTPS FTP |
-Related structure data
Related structure data | 2apgC 2aqjSC 2ardC C: citing same article (ref.) S: Starting model for refinement |
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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: 61146.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: PrnA / Plasmid: pPEH14 / Production host: Pseudomonas fluorescens (bacteria) / Strain (production host): Pseudomonas fluorescens BL915 / References: UniProt: P95480 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-CTE / |
#4: Chemical | ChemComp-FAD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 8% PEG20000, 0.1M Mes pH6.5, 20mM 7-chlorotryptophan, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→54.4 Å / Num. obs: 33547 / % possible obs: 99.7 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 1.8 / Redundancy: 14.1 % / Biso Wilson estimate: 29.25 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.2→2.32 Å / % possible obs: 98.7 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 4744 / Num. unique all: 4744 / Rsym value: 0.375 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AQJ Resolution: 2.2→54.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.518 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→54.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 9.882 Å / Origin y: 6.675 Å / Origin z: 20.117 Å
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Refinement TLS group | Selection: ALL |