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Yorodumi- PDB-2qo3: Crystal Structure of [KS3][AT3] didomain from module 3 of 6-deoxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qo3 | ||||||
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Title | Crystal Structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase | ||||||
Components | EryAII Erythromycin polyketide synthase modules 3 and 4 | ||||||
Keywords | TRANSFERASE / ketosynthase / acyltransferase / Phosphopantetheine | ||||||
Function / homology | Function and homology information 6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / transferase activity / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Saccharopolyspora erythraea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Khosla, C. / Cane, E.D. / Tang, Y. / Chen, Y.A. / Kim, C.Y. | ||||||
Citation | Journal: Chem.Biol. / Year: 2007 Title: Structural and mechanistic analysis of protein interactions in module 3 of the 6-deoxyerythronolide B synthase Authors: Tang, Y. / Chen, Y.A. / Kim, C.Y. / Cane, E.D. / Khosla, C. #1: Journal: Chem.Biol. / Year: 2007 Title: Structure-based dissociation of a type I polyketide synthase module Authors: Chen, Y.A. / Cane, E.D. / Khosla, C. #2: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase Authors: Tang, Y. / Kim, C.Y. / Mathews, I.I. / Cane, E.D. / Khosla, C. #3: Journal: Biochemistry / Year: 2004 Title: Reconstituting modular activity from separated domains of 6-deoxyerythronolide B synthase Authors: Kim, C.Y. / Alekseyev, V.Y. / Chen, Y.A. / Tang, Y. / Cane, E.D. / Khosla, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qo3.cif.gz | 330 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qo3.ent.gz | 271.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/2qo3 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/2qo3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-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 label comp-ID: SER / End label comp-ID: PHE / Refine code: 5 / Auth seq-ID: 30 - 900 / Label seq-ID: 5 - 875
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-Components
#1: Protein | Mass: 96689.180 Da / Num. of mol.: 2 Fragment: ketosynthase-acyltransferase didomain of didomain module 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAII / Plasmid: PAYC09 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: A4F7P0, UniProt: Q03132*PLUS, 6-deoxyerythronolide-B synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.66 Å3/Da / Density % sol: 53.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES pH7.0, 0.2M Li2SO4, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2005 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 228717 / Num. obs: 228471 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.09 / Num. unique all: 6207 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→41.52 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.877 / SU B: 23.423 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.817 / ESU R Free: 0.335 / 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: 21.862 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→41.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.595→2.662 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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