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Yorodumi- PDB-2v7u: X-ray crystal structure of 5'-fluorodeoxyadenosine synthase s158g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v7u | ||||||
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Title | X-ray crystal structure of 5'-fluorodeoxyadenosine synthase s158g mutant complexed with s-adenosylmethionine and chloride ion | ||||||
Components | 5'-FLUORO-5'-DEOXY ADENOSINE SYNTHETASE | ||||||
Keywords | TRANSFERASE / MECHANISM OF FLUORINATION / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES CATTLEYA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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 "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 | 2v7u.cif.gz | 194.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7u.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7u ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7u | HTTPS FTP |
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-Related structure data
Related structure data | 2v7tC 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) / Plasmid: PEHISTEV-FLAS158G / 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 | 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 0.1M CITRATE-PHOSPHATE BUFFER PH4.6, 20%(W/V) PEG1000, 0.2M LICL |
-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 IMAGE PLATE / Detector: IMAGE PLATE / Date: May 28, 2006 / Details: OSMIC MIRRORS |
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→30 Å / Num. obs: 55867 / % possible obs: 96 % / Observed criterion σ(I): 3.3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.3 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RQP Resolution: 2→30.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.531 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.154 / 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: 23.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30.7 Å
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Refine LS restraints |
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