[English] 日本語
Yorodumi- PDB-6l3m: Crystal Structure of the acyltransferase domain from the third mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l3m | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the acyltransferase domain from the third module of the ansamitocin polyketide synthase | ||||||
Components | Polyketide synthase | ||||||
Keywords | TRANSFERASE / Polyketide / acyltransferase / ACP-linked extender unit / carrier specificity / biosynthesis | ||||||
Function / homology | Function and homology information scavenger receptor activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / membrane Similarity search - Function | ||||||
Biological species | Actinosynnema pretiosum subsp. auranticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Zhang, F. / Zheng, J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Chembiochem / Year: 2020 Title: Structural and Biochemical Insight into the Recruitment of Acyl Carrier Protein-Linked Extender Units in Ansamitocin Biosynthesis. Authors: Zhang, F. / Ji, H. / Ali, I. / Deng, Z. / Bai, L. / Zheng, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6l3m.cif.gz | 340.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6l3m.ent.gz | 275.3 KB | Display | PDB format |
PDBx/mmJSON format | 6l3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l3m_validation.pdf.gz | 482.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6l3m_full_validation.pdf.gz | 488.6 KB | Display | |
Data in XML | 6l3m_validation.xml.gz | 67.5 KB | Display | |
Data in CIF | 6l3m_validation.cif.gz | 100.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/6l3m ftp://data.pdbj.org/pub/pdb/validation_reports/l3/6l3m | HTTPS FTP |
-Related structure data
Related structure data | 6j0uC 6l3nC 2hg4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44165.492 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinosynnema pretiosum subsp. auranticum (bacteria) Gene: AsmAT3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8KUH4*PLUS #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-E5U / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.2M K2HPO4 (pH 6) , 7% PEG 3350 (W/V) |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→98.54 Å / Num. obs: 186560 / % possible obs: 97.37 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 3 |
Reflection shell | Resolution: 1.77→98.54 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 186560 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HG4 Resolution: 1.77→98.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.669 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.58 Å2 / Biso mean: 20.072 Å2 / Biso min: 8.17 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.77→98.54 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.767→1.813 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|