[English] 日本語
Yorodumi- PDB-6apk: Trans-acting transferase from Disorazole synthase solved by seria... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6apk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Trans-acting transferase from Disorazole synthase solved by serial femtosecond XFEL crystallography | |||||||||
Components | DisD protein | |||||||||
Keywords | TRANSFERASE / Disorazole synthase / XFEL crystal structure / serial femtosecond crystallography | |||||||||
Function / homology | Function and homology information [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Sorangium cellulosum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | |||||||||
Authors | Lyubimov, A.Y. / Mathews, I.I. / Uervivojnangkoorn, M. / Khosla, C. / Soltis, S.M. / Cohen, A.E. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Biochemistry / Year: 2017 Title: The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography. Authors: Mathews, I.I. / Allison, K. / Robbins, T. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Brunger, A.T. / Khosla, C. / DeMirci, H. / McPhillips, S.E. / Hollenbeck, M. / Soltis, M. / Cohen, A.E. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6apk.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6apk.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 6apk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6apk_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6apk_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 6apk_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 6apk_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/6apk ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6apk | HTTPS FTP |
-Related structure data
Related structure data | 6apfC 6apgC 6apmC 3rgiS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30663.041 Da / Num. of mol.: 1 / Fragment: UNP residues 1-282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorangium cellulosum (bacteria) / Strain: SO CE12 / Gene: dszD, disD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q4U443, [acyl-carrier-protein] S-malonyltransferase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.6M Ammonium Sulphate, 100mM sodium citrate (pH 4.5) |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.3013 Å |
Detector | Type: RAYONIX MX170-HS / Detector: CCD / Date: Dec 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3013 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.5 Å / Num. obs: 10781 / % possible obs: 98.8 % / Redundancy: 14.2 % / Biso Wilson estimate: 3.09 Å2 / CC1/2: 0.92 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.79 / % possible all: 89.9 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Motion control: DCSS / Sample holding: Crystal/Sample Extractor |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RGI Resolution: 2.5→19.499 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 20.8 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.499 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|