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Yorodumi- PDB-4xs7: Determining the Molecular Basis for Starter Unit Selection During... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xs7 | ||||||
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Title | Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis | ||||||
Components | Daunorubicin-doxorubicin polyketide synthase | ||||||
Keywords | TRANSFERASE / polyketide / daunrubicin / starter unit | ||||||
Function / homology | Function and homology information secondary metabolite biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Streptomyces peucetius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Jackson, D.R. / Valentic, T.R. / Tsai, S.C. / Patel, A. / Mohammed, L. / Vasilakis, K. / Wattana-amorn, P. / Long, P.F. / Crump, M.P. / Crosby, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis Authors: Jackson, D.R. / Valentic, T.R. / Tsai, S.C. / Patel, A. / Mohammed, L. / Vasilakis, K. / Wattana-amorn, P. / Long, P.F. / Crump, M.P. / Crosby, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xs7.cif.gz | 143.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xs7.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 4xs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xs7_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 4xs7_full_validation.pdf.gz | 444.2 KB | Display | |
Data in XML | 4xs7_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 4xs7_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/4xs7 ftp://data.pdbj.org/pub/pdb/validation_reports/xs/4xs7 | HTTPS FTP |
-Related structure data
Related structure data | 4xs9C 4xsaC 4xsbC 4xqp 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: 39472.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Serine 118 is modified to an acetyl-serine residue / Source: (gene. exp.) Streptomyces peucetius (bacteria) / Gene: dpsC / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q54816, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.76 % Description: hexagonal crystals that look like Monopoly houses |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.18 M sodium citrate, 26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97753 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97753 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 31503 / % possible obs: 100 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4XQP 4xqp Resolution: 2.4→49.315 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.74 / 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: 2.4→49.315 Å
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Refine LS restraints |
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LS refinement shell |
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