[English] 日本語
Yorodumi- PDB-6c0y: Lysinoalanine synthase, DurN, from duramycin biosynthesis bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c0y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Lysinoalanine synthase, DurN, from duramycin biosynthesis bound to duramycin | |||||||||
Components |
| |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Lysinoalanine synthase / Michael addition | |||||||||
Function / homology | Protein of unknown function DUF5950 / Protein of unknown function DUF5973 / DurN substrate-assisted peptide maturase / Lantibiotic duramycin B-like / Duramycin / : / Lysinoalanine synthase / Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys-bh2-gly-asn-dbb-lys Function and homology information | |||||||||
Biological species | Streptomyces cinnamoneus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | |||||||||
Authors | Cogan, D.P. / Nair, S.K. | |||||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Substrate-assisted enzymatic formation of lysinoalanine in duramycin. Authors: An, L. / Cogan, D.P. / Navo, C.D. / Jimenez-Oses, G. / Nair, S.K. / van der Donk, W.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6c0y.cif.gz | 245.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6c0y.ent.gz | 195.2 KB | Display | PDB format |
PDBx/mmJSON format | 6c0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c0y_validation.pdf.gz | 552 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6c0y_full_validation.pdf.gz | 574.3 KB | Display | |
Data in XML | 6c0y_validation.xml.gz | 54.3 KB | Display | |
Data in CIF | 6c0y_validation.cif.gz | 80 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/6c0y ftp://data.pdbj.org/pub/pdb/validation_reports/c0/6c0y | HTTPS FTP |
-Related structure data
Related structure data | 6c0gC 6c0hSC 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: 13474.499 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Gene: durN / Plasmid: pET28a-MBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3F2YLX1*PLUS #2: Protein/peptide | #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.94 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 22.5% PEG 3350, 0.1 M MES pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.658→64.72 Å / Num. obs: 109913 / % possible obs: 95.8 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.039 / Rrim(I) all: 0.082 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.658→1.687 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5529 / CC1/2: 0.781 / Rpim(I) all: 0.387 / Rrim(I) all: 0.823 / % possible all: 95.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6C0H Resolution: 1.66→64.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.822 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 21.92 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.66→64.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|