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Yorodumi- PDB-2ard: The structure of tryptophan 7-halogenase (PrnA) suggests a mechan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ard | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 2ard.cif.gz | 117 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ard.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ard.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/2ard ftp://data.pdbj.org/pub/pdb/validation_reports/ar/2ard | HTTPS FTP |
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-Related structure data
Related structure data | 2apgC 2aqjC 2ar8SC 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-FDA / |
#3: 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: 52.4 % |
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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, 5mM FAD, 30mM sodium dithionite , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→54.82 Å / % possible obs: 98.2 % / Observed criterion σ(F): 11.5 / Observed criterion σ(I): 2.5 / Redundancy: 3.97 % / Biso Wilson estimate: 57.69 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.089 / Χ2: 0.81 / Net I/σ(I): 8 / Scaling rejects: 628 |
Reflection shell | Resolution: 2.59→2.69 Å / % possible obs: 96.3 % / Redundancy: 3.87 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.3 / Num. measured obs: 126 / Num. unique all: 1872 / Rsym value: 0.32 / Χ2: 0.9 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AR8 Resolution: 2.6→54.8 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 25.619 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.648 / ESU R Free: 0.332 / 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: 29.698 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→54.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.598→2.665 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 41.336 Å / Origin y: 23.754 Å / Origin z: 89.306 Å
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Refinement TLS group | Selection: ALL |