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Yorodumi- PDB-1rqp: Crystal structure and mechanism of a bacterial fluorinating enzyme -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rqp | ||||||
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Title | Crystal structure and mechanism of a bacterial fluorinating enzyme | ||||||
Components | 5'-fluoro-5'-deoxyadenosine synthase | ||||||
Keywords | TRANSFERASE / fluorinase / central 7 stranded beta sheets / anti-parallel beta sheets | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces cattleya (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Dong, C. / Huang, F. / Deng, H. / Schaffrath, C. / Spencer, J.B. / O'Hagan, D. / Naismith, J.H. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Crystal structure and mechanism of a bacterial fluorinating enzyme Authors: Dong, C. / Huang, F. / Deng, H. / Schaffrath, C. / Spencer, J.B. / O'Hagan, D. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and X-ray diffraction of 5'-fluoro-5'-deoxyadenosine synthase, a fluorination enzyme from Streptomyces cattleya Authors: Dong, C. / Deng, H. / Dorward, M. / Schaffrath, C. / O'Hagan, D. / 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 | 1rqp.cif.gz | 356.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rqp.ent.gz | 292.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqp ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqp | HTTPS FTP |
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-Related structure data
-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 on special symmetry positions |
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Details | The biological assembly is a hexamer generated from the trimer in the asymmetric unit |
-Components
#1: Protein | Mass: 32401.490 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Streptomyces cattleya (bacteria) / Strain: NRRL8057 / References: UniProt: Q70GK9, adenosyl-fluoride synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 22% PEG 1000, 0.1 M phosphate-citrate, 0.2 M Li2SO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7.8 / Method: vapor diffusion, sitting dropDetails: Dong, C., (2003) Acta Crystallogr.,Sect.D, 59, 2292. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933, 0.9786, 0.9783, 0.8984 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2002 / Details: Toroidal Zerodur mirror | |||||||||||||||
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→65 Å / Num. all: 84305 / Num. obs: 80164 / % possible obs: 94 % / Observed criterion σ(F): 1.33 / Observed criterion σ(I): 1.5 / Redundancy: 10 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.12 / Net I/σ(I): 2.8 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.847 Å / Redundancy: 6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1100 / Rsym value: 0.5 / % possible all: 70 | |||||||||||||||
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 65 Å / Num. obs: 67204 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 | |||||||||||||||
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.98 Å / % possible obs: 93 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→91.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.907 / SU ML: 0.089 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 1.3 / ESU R: 0.283 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→91.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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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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Refinement | *PLUS Highest resolution: 19 Å / Lowest resolution: 65 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.167 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.98 Å |