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- PDB-6ozv: The structure of condensation and adenylation domains of teixobac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ozv | ||||||
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Title | The structure of condensation and adenylation domains of teixobactin-producing nonribosomal peptide synthetase Txo1 serine module in complex with AMP | ||||||
![]() | Txo1 | ||||||
![]() | BIOSYNTHETIC PROTEIN / nonribosomal peptide synthetase / Teixobactin / Txo1 / Condensation domain / Adenylation Domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() toxin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / catalytic activity / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, K. / Zhou, M. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of teixobactin-producing nonribosomal peptide synthetase condensation and adenylation domains. Authors: Tan, K. / Zhou, M. / Jedrzejczak, R.P. / Wu, R. / Higuera, R.A. / Borek, D. / Babnigg, G. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 348.8 KB | Display | ![]() |
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PDB format | ![]() | 278.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 807.7 KB | Display | ![]() |
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Full document | ![]() | 819.6 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oyfSC ![]() 6p1jC ![]() 6p3iC ![]() 6p4uC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 96565.836 Da / Num. of mol.: 1 Fragment: Condensation and Adenylation Domain (UNP residues 2140-3009) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-AMP / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.05 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES/soldium chloride, 1.26 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→47.5 Å / Num. obs: 65631 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.035 / Rrim(I) all: 0.07 / Χ2: 0.887 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.18→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2757 / CC1/2: 0.688 / Rpim(I) all: 0.384 / Rrim(I) all: 0.731 / Χ2: 0.852 / % possible all: 82 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6OYF Resolution: 2.18→47.017 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→47.017 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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