+Open data
-Basic information
Entry | Database: PDB / ID: 5zw0 | ||||||
---|---|---|---|---|---|---|---|
Title | Apo-form PigA | ||||||
Components | L-prolyl-[peptidyl-carrier protein] dehydrogenase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / red pigment / pyrrole / acyl-CoA oxidase / FAD / tetramer | ||||||
Function / homology | Function and homology information L-prolyl-[peptidyl-carrier protein] dehydrogenase / 3-methylbutanoyl-CoA dehydrogenase activity / L-leucine catabolic process / antibiotic biosynthetic process / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Serratia sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Lee, C.-C. / Ko, T.-P. / Wang, A.H.J. | ||||||
Funding support | Taiwan, 1items
| ||||||
Citation | Journal: Chembiochem / Year: 2019 Title: Crystal Structure of PigA: A Prolyl Thioester-Oxidizing Enzyme in Prodigiosin Biosynthesis. Authors: Lee, C.-C. / Ko, T.-P. / Chen, C.T. / Chan, Y.T. / Lo, S.Y. / Chang, J.Y. / Chen, Y.W. / Chung, T.F. / Hsieh, H.J. / Hsiao, C.D. / Wang, A.H.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5zw0.cif.gz | 304.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5zw0.ent.gz | 247.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zw0_validation.pdf.gz | 445.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5zw0_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 5zw0_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 5zw0_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/5zw0 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/5zw0 | HTTPS FTP |
-Related structure data
Related structure data | 5zw2C 5zw7C 5zw8C 6af6C 4l1fS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43950.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia sp. (strain ATCC 39006) (bacteria) Strain: ATCC 39006 / Gene: pigA / Production host: Escherichia coli (E. coli) References: UniProt: Q5W271, L-prolyl-[peptidyl-carrier protein] dehydrogenase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 27% polyethylene glycol 600, 0.1M Na-HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 28, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→20 Å / Num. obs: 31276 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.54→2.64 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3093 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L1F Resolution: 2.54→19.9 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.89
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→19.9 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 17.9299 Å / Origin y: 17.3281 Å / Origin z: -4.5382 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |