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Yorodumi- PDB-5ing: A crotonyl-CoA reductase-carboxylase independent pathway for asse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ing | ||||||||||||
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Title | A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender unit | ||||||||||||
Components | Putative carboxyl transferase | ||||||||||||
Keywords | TRANSFERASE / Acyl-CoA / Crotonase / Polyketide / 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: 2.45 Å | ||||||||||||
Authors | Valentic, T.R. / Ray, L. / Miyazawa, T. / Song, L. / Withall, D.M. / Milligan, J.C. / Takahashi, S. / 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 | 5ing.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ing.ent.gz | 967.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ing.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ing_validation.pdf.gz | 507.1 KB | Display | wwPDB validaton report |
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Full document | 5ing_full_validation.pdf.gz | 554.4 KB | Display | |
Data in XML | 5ing_validation.xml.gz | 111.1 KB | Display | |
Data in CIF | 5ing_validation.cif.gz | 155.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/5ing ftp://data.pdbj.org/pub/pdb/validation_reports/in/5ing | HTTPS FTP |
-Related structure data
Related structure data | 5infC 5iniC 3ibbS C: citing same article (ref.) 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: 62409.812 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: 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: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 6-11% MPD (2-Methyl-2,4-pentanediol), 0.2 M magnesium acetate, and 0.1 M MES pH 6.6-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2014 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→81.72 Å / Num. obs: 134126 / % possible obs: 99 % / Redundancy: 6.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 1.6 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IBB Resolution: 2.45→81.72 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.58 / 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: 2.45→81.72 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 169.037 Å / Origin y: 5.7567 Å / Origin z: 5.3934 Å
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Refinement TLS group | Selection details: all |