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Yorodumi- PDB-2v7t: X-ray crystal structure of 5'-fluorodeoxyadenosine synthase s158g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v7t | ||||||
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Title | X-ray crystal structure of 5'-fluorodeoxyadenosine synthase s158g mutant complexed with s-adenosyl-l-homocysteine and chloride ion | ||||||
Components | 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE | ||||||
Keywords | TRANSFERASE / MECHANISM OF FLUORINATION / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES CATTLEYA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | 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 "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7t.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7t.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 2v7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7t ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7t | HTTPS FTP |
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-Related structure data
Related structure data | 2v7uC 2v7vC 2v7wC 2v7xC 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: 32371.467 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CATTLEYA (bacteria) / Strain: NRRL8057 / Plasmid: PEHISTEV / 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 GLY ENGINEERED RESIDUE IN CHAIN B, SER 158 TO GLY ...ENGINEERED | |
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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 0.1M CITRATE-PHOSPHATE BUFFER PH4.6, 18%(W/V)PEG1000, 0.2M LICL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37.2 Å / Num. obs: 45152 / % possible obs: 97 % / Observed criterion σ(I): 2.4 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RQP Resolution: 2.15→36.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.832 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.186 / 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: 31.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→36.94 Å
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Refine LS restraints |
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