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Open data
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Basic information
Entry | Database: PDB / ID: 4tx3 | ||||||
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Title | Complex of the X-domain and OxyB from Teicoplanin Biosynthesis | ||||||
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![]() | OXIDOREDUCTASE / non-ribosomal peptide synthetase / condensation-type domain / teicoplanin biosynthesis / oxygenase complex / hydrolase | ||||||
Function / homology | ![]() biosynthetic process / hydrolase activity, acting on ester bonds / glycosyltransferase activity / phosphopantetheine binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peschke, M. / Haslinger, K. / Cryle, M.J. | ||||||
![]() | ![]() Title: X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis. Authors: Haslinger, K. / Peschke, M. / Brieke, C. / Maximowitsch, E. / Cryle, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.7 KB | Display | ![]() |
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PDB format | ![]() | 140.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 826.3 KB | Display | ![]() |
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Full document | ![]() | 832.2 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 46.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tx2SC ![]() 4tvfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 44494.746 Da / Num. of mol.: 1 / Fragment: UNP residues 1-398 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: tcp20 / Plasmid: pET24d / Details (production host): GB1-fusion protein / Production host: ![]() ![]() |
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#2: Protein | Mass: 53435.977 Da / Num. of mol.: 1 / Fragment: UNP residues 1047-1511 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: teiD / Plasmid: pET151d / Details (production host): TOPO plasmid / Production host: ![]() ![]() |
-Non-polymers , 4 types, 259 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-HEM / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Bis-Tris, 200 mM (NH4)2SO4, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 36333 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 40.38 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.093 / Χ2: 0.973 / Net I/σ(I): 14.96 / Num. measured all: 212554 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TX2, 4TVF Resolution: 2.5→47.005 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.69 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.42 Å2 / Biso mean: 43.5361 Å2 / Biso min: 21.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→47.005 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %
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