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Yorodumi- PDB-6c9u: Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c9u | ||||||
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Title | Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase in complex with antibody fragment (Fab) | ||||||
Components |
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Keywords | TRANSFERASE/immune system / DEBS / PKS / polyketide synthase / 6-deoxyerthronolide B synthase / Fab / antibody / phage display / TRANSFERASE-immune system complex | ||||||
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 / fatty acid biosynthetic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Saccharopolyspora erythraea (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Deis, L.N. / Li, X. / Mathews, I.I. / Khosla, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Structure-Function Analysis of the Extended Conformation of a Polyketide Synthase Module. Authors: Li, X. / Sevillano, N. / La Greca, F. / Deis, L. / Liu, Y.C. / Deller, M.C. / Mathews, I.I. / Matsui, T. / Cane, D.E. / Craik, C.S. / Khosla, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c9u.cif.gz | 485.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c9u.ent.gz | 396.8 KB | Display | PDB format |
PDBx/mmJSON format | 6c9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/6c9u ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c9u | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 99797.750 Da / Num. of mol.: 1 / Fragment: [KS3][AT3] didomain from module 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryA / Production host: Escherichia coli (E. coli) References: UniProt: Q03132, 6-deoxyerythronolide-B synthase |
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-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 25715.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#3: Antibody | Mass: 26447.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 3 types, 683 molecules
#4: Chemical | ChemComp-K / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.86 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 200 mM potassium citrate, 20%(w/v) PEG 3,350 and 12% ethylene glycol) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.092→46.08 Å / Num. obs: 93106 / % possible obs: 93.9 % / Redundancy: 7.4 % / Net I/σ(I): 2.44 |
Reflection shell | Resolution: 2.09→2.17 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QO3, 1SBS Resolution: 2.09→46.08 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→46.08 Å
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Refine LS restraints |
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LS refinement shell |
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