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Yorodumi- PDB-5ini: Structural basis for acyl-CoA carboxylase-mediated assembly of un... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ini | ||||||||||||
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Title | Structural basis for acyl-CoA carboxylase-mediated assembly of unusual polyketide synthase extender units incorporated into the stambomycin antibiotics | ||||||||||||
Components | Putative carboxyl transferase | ||||||||||||
Keywords | TRANSFERASE / Polyketide / Acyl-CoA / Crotonase / Extender-Unit | ||||||||||||
Function / homology | Function and homology information propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / transferase activity Similarity search - Function | ||||||||||||
Biological species | Streptomyces ambofaciens ATCC 23877 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||||||||
Authors | Valentic, T.R. / Ray, L. / Miyazawa, T. / Withall, D.M. / Song, L. / Milligan, J.C. / Osada, H. / Tsai, S.C. / Challis, G.L. | ||||||||||||
Funding support | United Kingdom, United States, 3items
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Citation | Journal: Nat Commun / Year: 2016 Title: A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units. Authors: Ray, L. / Valentic, T.R. / Miyazawa, T. / Withall, D.M. / Song, L. / Milligan, J.C. / Osada, H. / Takahashi, S. / Tsai, S.C. / Challis, G.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ini.cif.gz | 563.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ini.ent.gz | 460.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ini.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ini_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5ini_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5ini_validation.xml.gz | 107.7 KB | Display | |
Data in CIF | 5ini_validation.cif.gz | 144.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/5ini ftp://data.pdbj.org/pub/pdb/validation_reports/in/5ini | HTTPS FTP |
-Related structure data
Related structure data | 5infC 5ingSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58100.641 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces ambofaciens ATCC 23877 (bacteria) Gene: SAM23877_7108, SAMR0483 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0ACI9 #2: Chemical | ChemComp-HXC / #3: 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: 2.41 Å3/Da / Density % sol: 48.91 % / Description: Rod shaped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 26-32% PEG 5000 MME, 0.2 M ammonium sulfate and 0.1 M MES pH 6.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2015 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→58.245 Å / Num. obs: 79293 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.206 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.85→2.91 Å / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 3.6 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ING Resolution: 2.85→58.233 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→58.233 Å
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Refine LS restraints |
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LS refinement shell |
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