+Open data
-Basic information
Entry | Database: PDB / ID: 5dlk | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of CT mutant | ||||||
Components | TqaA | ||||||
Keywords | UNKNOWN FUNCTION / Biochemistry / mutant | ||||||
Function / homology | Function and homology information : / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / cytoplasm Similarity search - Function | ||||||
Biological species | Penicillium aethiopicum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zhang, J.R. / Tang, Y. / Zhou, J.H. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Structural basis of nonribosomal peptide macrocyclization in fungi Authors: Zhang, J. / Liu, N. / Cacho, R.A. / Gong, Z. / Liu, Z. / Qin, W. / Tang, C. / Tang, Y. / Zhou, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5dlk.cif.gz | 391.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5dlk.ent.gz | 317.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dlk_validation.pdf.gz | 495.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5dlk_full_validation.pdf.gz | 506.7 KB | Display | |
Data in XML | 5dlk_validation.xml.gz | 76 KB | Display | |
Data in CIF | 5dlk_validation.cif.gz | 111.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlk ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlk | HTTPS FTP |
-Related structure data
Related structure data | 5dijSC 5egfC 5ejdC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 53670.582 Da / Num. of mol.: 4 / Fragment: UNP residues 3595-4074 / Mutation: residues 3992-4001 deletion mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium aethiopicum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F1CWE4 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-DMS / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.79 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Sodium malnate, Bis-Tris propane, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 256485 / % possible obs: 99.9 % / Redundancy: 5.6 % / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DIJ Resolution: 1.8→41.906 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.86 / 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: 1.8→41.906 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|