+Open data
-Basic information
Entry | Database: PDB / ID: 4tx3 | ||||||
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Title | Complex of the X-domain and OxyB from Teicoplanin Biosynthesis | ||||||
Components |
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Keywords | OXIDOREDUCTASE / non-ribosomal peptide synthetase / condensation-type domain / teicoplanin biosynthesis / oxygenase complex / hydrolase | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / biosynthetic process / hydrolase activity, acting on ester bonds / glycosyltransferase activity / steroid hydroxylase activity / phosphopantetheine binding / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Actinoplanes teichomyceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Peschke, M. / Haslinger, K. / Cryle, M.J. | ||||||
Citation | Journal: Nature / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tx3.cif.gz | 184.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tx3.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 4tx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/4tx3 ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4tx3 | HTTPS FTP |
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-Related structure data
Related structure data | 4tx2SC 4tvfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Actinoplanes teichomyceticus (bacteria) Gene: tcp20 / Plasmid: pET24d / Details (production host): GB1-fusion protein / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70AY8, unspecific monooxygenase |
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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.) Actinoplanes teichomyceticus (bacteria) Gene: teiD / Plasmid: pET151d / Details (production host): TOPO plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6ZZJ3 |
-Non-polymers , 4 types, 259 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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