+Open data
-Basic information
Entry | Database: PDB / ID: 6m7l | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Complex of OxyA with the X-domain from GPA biosynthesis | ||||||||||||
Components |
| ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / NRPS / P450 / GPAs / monooxygenase / X-domain | ||||||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / biosynthetic process / phosphopantetheine binding / catalytic activity / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||||||||
Biological species | Actinomadura parvosata subsp. kistnae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64829708903 Å | ||||||||||||
Authors | Greule, A. / Izore, T. / Tailhades, J. / Peschke, M. / Schoppet, M. / Ahmed, I. / Kulik, A. / Adamek, M. / Ziemert, N. / De Voss, J. ...Greule, A. / Izore, T. / Tailhades, J. / Peschke, M. / Schoppet, M. / Ahmed, I. / Kulik, A. / Adamek, M. / Ziemert, N. / De Voss, J. / Stegmann, E. / Cryle, M.J. | ||||||||||||
Funding support | Australia, Germany, 3items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics. Authors: Greule, A. / Izore, T. / Iftime, D. / Tailhades, J. / Schoppet, M. / Zhao, Y. / Peschke, M. / Ahmed, I. / Kulik, A. / Adamek, M. / Goode, R.J.A. / Schittenhelm, R.B. / Kaczmarski, J.A. / ...Authors: Greule, A. / Izore, T. / Iftime, D. / Tailhades, J. / Schoppet, M. / Zhao, Y. / Peschke, M. / Ahmed, I. / Kulik, A. / Adamek, M. / Goode, R.J.A. / Schittenhelm, R.B. / Kaczmarski, J.A. / Jackson, C.J. / Ziemert, N. / Krenske, E.H. / De Voss, J.J. / Stegmann, E. / Cryle, M.J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6m7l.cif.gz | 209.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6m7l.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 6m7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m7l_validation.pdf.gz | 797.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6m7l_full_validation.pdf.gz | 809 KB | Display | |
Data in XML | 6m7l_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 6m7l_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/6m7l ftp://data.pdbj.org/pub/pdb/validation_reports/m7/6m7l | HTTPS FTP |
-Related structure data
Related structure data | 4tx3S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53594.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinomadura parvosata subsp. kistnae (bacteria) Gene: KIS93_04814 / Production host: Escherichia coli (E. coli) / Strain (production host): ArticExpress / References: UniProt: A0A2P9IBG7 |
---|---|
#2: Protein | Mass: 44949.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinomadura parvosata subsp. kistnae (bacteria) Gene: KIS93_04812 / Production host: Escherichia coli (E. coli) / Strain (production host): ArticExpress / References: UniProt: A0A2P9IBF7 |
#3: Chemical | ChemComp-HEM / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % |
---|---|
Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG3350 300 mM NaCl 100 mM BIS-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→48.14 Å / Num. obs: 28454 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 64.8360834054 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.035 / Rrim(I) all: 0.052 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3722 / CC1/2: 0.837 / Rpim(I) all: 0.464 / % possible all: 98.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TX3 Resolution: 2.64829708903→47.7345054735 Å / SU ML: 0.384661428753 / Cross valid method: FREE R-VALUE / σ(F): 1.34748235633 / Phase error: 30.2165510926
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.1223540858 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64829708903→47.7345054735 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|