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Yorodumi- PDB-1rqr: Crystal structure and mechanism of a bacterial fluorinating enzym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rqr | |||||||||
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Title | Crystal structure and mechanism of a bacterial fluorinating enzyme, product complex | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.67 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.J. / 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 | 1rqr.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rqr.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqr ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqr | 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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Details | The biological assembly is a hexamer generated from the trimer in the asymmetric unit |
-Components
#1: Protein | Mass: 32682.861 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cattleya (bacteria) / Gene: fla / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q70GK9, adenosyl-fluoride synthase #2: Chemical | #3: Chemical | #4: 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: 2.32 Å3/Da / Density % sol: 46.96 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 22% PEG 1000, 0.1M phosphate-citrate, 0.2M 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: BM14 / Wavelength: 0.9786 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 8, 2003 / Details: 2 Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→53.64 Å / Num. all: 26303 / Num. obs: 26003 / % possible obs: 99 % / Observed criterion σ(F): 5.967 / Observed criterion σ(I): 5.4 / Redundancy: 6.3 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.064 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.67→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1821 / Rsym value: 0.133 / % possible all: 99 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 53 Å / Num. obs: 26303 / % possible obs: 97 % / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 81 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 4.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→91.29 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 10.333 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 5.96 / σ(I): 3.5 / ESU R Free: 0.335 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.058 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→91.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.67→2.742 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: 2.7 Å / Lowest resolution: 53 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.74 Å |