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Yorodumi- PDB-2v7x: X-RAY CRYSTAL STRUCTURE OF 5'-FLUORODEOXYADENOSINE SYNTHASE S158A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v7x | |||||||||
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Title | X-RAY CRYSTAL STRUCTURE OF 5'-FLUORODEOXYADENOSINE SYNTHASE S158A mutant FROM STREPTOMYCES CATTLEYA COMPLEXED WITH the PRODUCTS, FDA and Met | |||||||||
Components | 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE | |||||||||
Keywords | TRANSFERASE / FLUORINASE / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | STREPTOMYCES CATTLEYA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | |||||||||
Authors | Robinson, D.A. / Zhu, X. / O'Hagan, D. / Naismith, J.H. | |||||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2007 Title: Mechanism of enzymatic fluorination in Streptomyces cattleya. Authors: Zhu, X. / Robinson, D.A. / McEwan, A.R. / O'Hagan, D. / Naismith, J.H. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7x.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7x.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 2v7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7x ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7x | HTTPS FTP |
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-Related structure data
Related structure data | 2v7tC 2v7uC 2v7vC 2v7wC 1rqpS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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-Components
#1: Protein | Mass: 32385.494 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CATTLEYA (bacteria) / Plasmid: PEHISTEV-FLAS158A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q70GK9, adenosyl-fluoride synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 158 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 158 TO ALA ...ENGINEERED | Sequence details | SITE DIRECTED MUTAGENESI | |
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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 4.2 Details: 0.1M CITRATE-PHOSPHATE BUFFER PH4.2, 24%PEG1000, 0.2M LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2005 / Details: RH COATED SI MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.4 Å / Num. obs: 47782 / % possible obs: 82.2 % / Observed criterion σ(I): 4 / Redundancy: 5.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.2 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RQP Resolution: 1.96→35.2 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.39 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.183 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→35.2 Å
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Refine LS restraints |
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