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Yorodumi- PDB-1mzj: Crystal Structure of the Priming beta-Ketosynthase from the R1128... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mzj | ||||||
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Title | Crystal Structure of the Priming beta-Ketosynthase from the R1128 Polyketide Biosynthetic Pathway | ||||||
Components | Beta-ketoacylsynthase III | ||||||
Keywords | TRANSFERASE / beta-Ketosynthase / aromatic polyketide / biosynthetic engineering / catalytic triad | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces sp. R1128 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Pan, H. / Tsai, S.C. / Meadows, E.S. / Miercke, L.J.W. / Keatinge-Clay, A. / O'Connell, J. / Khosla, C. / Stroud, R.M. | ||||||
Citation | Journal: Structure Title: Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway Authors: Pan, H. / Tsai, S. / Meadows, E.S. / Miercke, L.J. / Keatinge-Clay, A.T. / O'Connell, J. / Khosla, C. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mzj.cif.gz | 138.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mzj.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/1mzj ftp://data.pdbj.org/pub/pdb/validation_reports/mz/1mzj | HTTPS FTP |
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-Related structure data
Related structure data | 1eblS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 35428.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. R1128 (bacteria) / Gene: zhuH / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9F6D4, beta-ketoacyl-[acyl-carrier-protein] synthase I #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: 2.72 Å3/Da / Density % sol: 54.85 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 8000, sodium cacodylate, magnesium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2000 / Details: Flat mirror + single crystal Si(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 43722 / Num. obs: 43722 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.057 / Rsym value: 0.055 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / Num. unique all: 2231 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å / Redundancy: 6.1 % / Num. measured all: 264571 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EBL Resolution: 2.1→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→500 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 41952 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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