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Yorodumi- PDB-2f99: Crystal structure of the polyketide cyclase AknH with bound subst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f99 | ||||||
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Title | Crystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity. | ||||||
Components | Aklanonic Acid methyl Ester Cyclase, AknH | ||||||
Keywords | BIOSYNTHETIC PROTEIN / anthracycline / polyketide cyclase / stereoselectivity / aklavinone | ||||||
Function / homology | Function and homology information aklanonic acid methyl ester cyclase / intramolecular lyase activity / daunorubicin biosynthetic process / doxorubicin metabolic process / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces galilaeus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kallio, P. / Sultana, A. / Neimi, J. / Mantsala, P. / Schneider, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity. Authors: Kallio, P. / Sultana, A. / Niemi, J. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f99.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f99.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 2f99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/2f99 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/2f99 | HTTPS FTP |
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-Related structure data
Related structure data | 2f98SC 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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3 |
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Unit cell |
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Details | Biological assembly is a tetramer. There are also four molecules in the assymetric unit which forms tetramer by generating the symmetric molecules with the symmetry operator 0,-1,-1 and 1,0,-1 |
-Components
#1: Protein | Mass: 17951.146 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces galilaeus (bacteria) / Plasmid: pBAD/HisB / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: GenBank: 7800671, UniProt: O52646*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-AKV / { #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: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.0M ammonium Chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2004 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→84.52 Å / Num. all: 73655 / Num. obs: 73655 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.056 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.9→1.95 Å / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2F98 Resolution: 1.9→84.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.744 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.11 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.095 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→84.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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