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- PDB-2cc2: X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cc2 | ||||||
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Title | X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with 5'deoxyadenosine | ||||||
![]() | 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mcewan, A.R. / Deng, H. / McGlinchey, R.P. / Robinson, D.R. / O'Hagan, D. / Spencer, J. / Naismith, J.H. | ||||||
![]() | ![]() Title: Substrate specificity in enzymatic fluorination. The fluorinase from Streptomyces cattleya accepts 2'-deoxyadenosine substrates. Authors: Cobb, S.L. / Deng, H. / McEwan, A.R. / Naismith, J.H. / O'Hagan, D. / Robinson, D.A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.8 KB | Display | ![]() |
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PDB format | ![]() | 270.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2c4uC ![]() 2c5bC ![]() 2cbxC ![]() 2c2wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 20 - 290 / Label seq-ID: 20 - 290
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Components
#1: Protein | Mass: 32401.490 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-CL / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.28 % |
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Crystal grow![]() | pH: 4 Details: 24% PEG 1K, 100MM PHOSPHATE CITRATE PH4.4, 200MM LI2SO4, 20MM NACL, pH 4.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 21, 2005 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND 111-GE-20 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→44.9 Å / Num. obs: 45862 / % possible obs: 74.1 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.1 / % possible all: 66.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2C2W Resolution: 2→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.36 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35 Å
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Refine LS restraints |
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