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Yorodumi- PDB-2c5b: X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c5b | ||||||
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Title | X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with 2'deoxy-5'deoxy-fluoroadenosine. | ||||||
Components | 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE | ||||||
Keywords | TRANSFERASE / FLUORINASE / 5'-FLUORODEOXYADENOSINE SYNTHASE / FLA / INHIBITOR / AZA / STREPTOMYCES CATTLEYA / SAM ANALOGUE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES CATTLEYA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | McEwan, A.R. / Deng, H. / McGlinchey, R.P. / Robinson, D.A. / O'Hagan, D. / Naismith, J.H. / Spencer, J. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2006 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 "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 | 2c5b.cif.gz | 178.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c5b.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 2c5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c5b_validation.pdf.gz | 523.2 KB | Display | wwPDB validaton report |
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Full document | 2c5b_full_validation.pdf.gz | 554.9 KB | Display | |
Data in XML | 2c5b_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 2c5b_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/2c5b ftp://data.pdbj.org/pub/pdb/validation_reports/c5/2c5b | HTTPS FTP |
-Related structure data
Related structure data | 2c4uC 2cbxC 2cc2C 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: Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 20 - 270 / Label seq-ID: 20 - 270
NCS ensembles :
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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.) STREPTOMYCES CATTLEYA (bacteria) / Plasmid: PEHISTEV-FLA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): 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: 2.37 Å3/Da / Density % sol: 49 % |
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Crystal grow | pH: 4 Details: 32%PEG 1K, 100MM PHOSPHATECITRATE PH4.2, 200MM LI2SO4, pH 4.00 |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RAXIS / Detector: IMAGE PLATE / Date: May 17, 2005 / 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: 2.5→37.69 Å / Num. obs: 27454 / % possible obs: 87 % / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.4 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RQP Resolution: 2.5→37 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.864 / SU B: 19.697 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→37 Å
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Refine LS restraints |
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