[English] 日本語
Yorodumi- PDB-5isx: Structure of the holo PCP-E didomain of the gramicidin S synthetase A -
+Open data
-Basic information
Entry | Database: PDB / ID: 5isx | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the holo PCP-E didomain of the gramicidin S synthetase A | ||||||
Components | Gramicidin S synthase 1 | ||||||
Keywords | ISOMERASE / Epimerization domain / NRPS / gramicidin S | ||||||
Function / homology | Function and homology information phenylalanine racemase (ATP-hydrolysing) / phenylalanine racemase (ATP-hydrolyzing) activity / : / ligase activity / antibiotic biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Brevibacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.335 Å | ||||||
Authors | Chen, W.-H. / Li, K. / Bruner, S.D. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Interdomain and Intermodule Organization in Epimerization Domain Containing Nonribosomal Peptide Synthetases. Authors: Chen, W.H. / Li, K. / Guntaka, N.S. / Bruner, S.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5isx.cif.gz | 235.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5isx.ent.gz | 193.4 KB | Display | PDB format |
PDBx/mmJSON format | 5isx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/5isx ftp://data.pdbj.org/pub/pdb/validation_reports/is/5isx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 67238.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: grsA, grs1 / Production host: Escherichia coli (E. coli) References: UniProt: P0C062, phenylalanine racemase (ATP-hydrolysing) #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.19 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M MgCl2, 18% PEG 3350, 5% glycerol, and 100 mM sodium cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.335→38.971 Å / % possible obs: 99.3 % / Redundancy: 7.7 % / Net I/σ(I): 3.38 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.335→38.971 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / 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: 2.335→38.971 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|